Split-off dimer defects on the Si(001)2x1 surface

Dimer vacancy (DV) defect complexes in the Si(001)2x1 surface were investigated using high-resolution scanning tunneling microscopy and first principles calculations. We find that under low bias filled-state tunneling conditions, isolated 'split-off' dimers in these defect complexes are imaged as pairs of protrusions while the surrounding Si surface dimers appear as the usual 'bean-shaped' protrusions. We attribute this to the formation of pi-bonds between the two atoms of the split-off dimer and second layer atoms, and present charge density plots to support this assignment. We observe a local brightness enhancement due to strain for different DV complexes and provide the first experimental confirmation of an earlier prediction that the 1+2-DV induces less surface strain than other DV complexes. Finally, we present a previously unreported triangular shaped split-off dimer defect complex that exists at SB-type step edges, and propose a structure for this defect involving a bound Si monomer.Comment: 8 pages, 7 figures, submitted to Phys. Rev.

Contextualizing instruction: Leveraging students' prior knowledge and experiences to foster understanding of middle school science

Contextualizing science instruction involves utilizing students' prior knowledge and everyday experiences as a catalyst for understanding challenging science concepts. This study of two middle school science classrooms examined how students utilized the contextualizing aspects of project-based instruction and its relationship to their science learning. Observations of focus students' participation during instruction were described in terms of a contextualizing score for their use of the project features to support their learning. Pre/posttests were administered and students' final artifacts were collected and evaluated. The results of these assessments were compared with students' contextualizing scores, demonstrating a strong positive correlation between them. These findings provide evidence to support claims of contextualizing instruction as a means to facilitate student learning, and point toward future consideration of this instructional method in broader research studies and the design of science learning environments. © 2007 Wiley Periodicals, Inc. J Res Sci Teach 45: 79–100, 2008Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/57510/1/20203_ftp.pd

Multimodal therapy in an inpatient setting

Inpatient Multimodal Therapy (imt) is a residential treatment program, lasting a maximum of 36 weeks, for patients with severe neurotic symptoms. A group of 44 chronic obsessive-compulsive patients and a group of 40 chronic phobic patients were treated in order to assess the outcome and the process of treatment and to identify prognostic factors associated with the effect. At follow-up-on average, eight months after discharge-it was found that 60% had improved, 32% had remained the same, and 8% had deteriorated, indicating that, in general, the treatment was beneficial. That these effects were long-lasting is supported by the fact that, at follow-up, 78% of all patients were no longer receiving treatment, 18% were receiving outpatient or day treatment, and 4% were receiving inpatient treatment. Phobic patients appear to have gained more from the multimodal approach than did obsessive-compulsive patients, as indicated by the fact that the severity of symptoms decreased as they improved in rational thinking, assertiveness, and arousal. By contrast, obsessive-compulsive patients relapsed more than phobic patients did. This was attributed to the fact that the former gained less from the rational-emotive training, denied problems with assertiveness, and did not practice the acquired relaxation skills. It further appeared that a favorable outcome could be induced in patients who (1) expressed relatively mild symptoms in this otherwise severe group, (2) reported relatively few additional complaints, (3) could clearly indicate interpersonal problems, and (4) did not use psychotropic drugs. These prognostic factors are so widespread that not much weight can be ascribed to them. Yet they are useful for indication of imt until better predictors are found

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Repurposing an integrated national influenza platform for genomic surveillance of SARS-CoV-2 in Ghana: a molecular epidemiological analysis

Background Genomic surveillance of SARS-CoV-2 is crucial for monitoring the spread of COVID-19 and guiding public health decisions, but the capacity for SARS-CoV-2 testing and sequencing in Africa is low. We integrated SARS-CoV-2 surveillance into an existing influenza surveillance network with the aim of providing insights into SARS-CoV-2 transmission and genomics in Ghana. Methods In this molecular epidemiological analysis, which is part of a wider multifaceted prospective observational study, we collected national SARS-CoV-2 test data from 35 sites across 16 regions in Ghana from Sept 1, 2020, to Nov 30, 2021, via the Ghanaian integrated influenza and SARS-CoV-2 surveillance network. SARS-CoV-2-positive samples collected through this integrated national influenza surveillance network and from international travellers arriving in Accra were sequenced with Oxford Nanopore Technology sequencing and the ARTIC tiled amplicon method. The sequence lineages were typed with pangolin and the phylogenetic analysis was conducted with IQ-Tree2 and TreeTime. Findings During the study period, 5495 samples were submitted for diagnostic testing through the national influenza surveillance network (2121 [46·1%] of 4021 samples with complete demographic data were from female individuals and 2479 [53·9%] of 4021 samples were from male individuals). We also obtained 2289 samples from travellers who arrived in Accra and had a positive lateral flow test, of whom 1626 (71·0%, 95% CI 69·1–72·9) were confirmed to be SARS-CoV-2 positive. Co-circulation of influenza and SARS-CoV-2 in Ghana was detected, with increased cases of influenza in November, 2020, November, 2021, and January and June, 2021. In 4124 samples from individuals with influenza-like illness, SARS-CoV-2 was identified in 583 (14·1%, 95% CI 13·1–15·2) samples and influenza in 356 (8·6%, 7·8–9·5). Conversely, in 476 samples from individuals with of severe acute respiratory illness, SARS-CoV-2 was detected in 58 (12·2%, 9·5–15·5) samples and influenza in 95 (19·9%, 16·5–23·9). We detected four waves of SARS-CoV-2 infections in Ghana; each wave was driven by a different variant: B.1 and B.1.1 were the most prevalent lineages in wave 1, alpha (B.1.1.7) was responsible for wave 2, delta (B.1.617.2) and its sublineages (closely related to delta genomes from India) were responsible for wave 3, and omicron variants were responsible for wave 4. We detected omicron variants among 47 (32%) of 145 samples from travellers during the start of the omicron spread in Ghana (wave 4). Interpretation This study shows the value of repurposing existing influenza surveillance platforms to monitor SARS-CoV-2. Influenza continued to circulate in Ghana in 2020 and 2021, and remained a major cause of severe acute respiratory illness. We detected importations of SARS-CoV-2 variants into Ghana, including those that did or did not lead to onward community transmission. Investment in strengthening national influenza surveillance platforms in low-income and middle-income countries has potential for ongoing monitoring of SARS-CoV-2 and future pandemics. Funding The EDCTP2 programme supported by the EU

The boomerang effect of radicalism in Discursive Psychology: A critical overview of the controversy with the Social Representations Theory.

This article provides a critical overview of the controversy between the Radical approach to Discursive Psychology (RDP) and the Social Representations Theory (SRT) and aims: a)?to show what is potentially complementary and contradictory in Discursive Psychology (DP) and the Social Representations Theory, when and why they are incompatible, and whether and how it is possible and/or desirable to integrate these two approaches. b)?to describe how the radicalism of the socio-constructionist thesis upheld by Discourse Analysis can give rise to several hard-to-solve problems, which may then be translated into a boomerang effect. In the final section, it highlights interest in dialog and “cross-fertilization” between researchers inspired by the less radical approach to discursive psychology and those inspired by the Social Representations Theory, pointing out the effect of methodological implications that would ensue

Driver Fusions and Their Implications in the Development and Treatment of Human Cancers.

Gene fusions represent an important class of somatic alterations in cancer. We systematically investigated fusions in 9,624 tumors across 33 cancer types using multiple fusion calling tools. We identified a total of 25,664 fusions, with a 63% validation rate. Integration of gene expression, copy number, and fusion annotation data revealed that fusions involving oncogenes tend to exhibit increased expression, whereas fusions involving tumor suppressors have the opposite effect. For fusions involving kinases, we found 1,275 with an intact kinase domain, the proportion of which varied significantly across cancer types. Our study suggests that fusions drive the development of 16.5% of cancer cases and function as the sole driver in more than 1% of them. Finally, we identified druggable fusions involving genes such as TMPRSS2, RET, FGFR3, ALK, and ESR1 in 6.0% of cases, and we predicted immunogenic peptides, suggesting that fusions may provide leads for targeted drug and immune therapy

Global, regional, and national comparative risk assessment of 79 behavioural, environmental and occupational, and metabolic risks or clusters of risks, 1990-2015: A systematic analysis for the Global Burden of Disease Study 2015

Background: The Global Burden of Diseases, Injuries, and Risk Factors Study 2015 provides an up-to-date synthesis of the evidence for risk factor exposure and the attributable burden of disease. By providing national and subnational assessments spanning the past 25 years, this study can inform debates on the importance of addressing risks in context. Methods: We used the comparative risk assessment framework developed for previous iterations of the Global Burden of Disease Study to estimate attributable deaths, disability-adjusted life-years (DALYs), and trends in exposure by age group, sex, year, and geography for 79 behavioural, environmental and occupational, and metabolic risks or clusters of risks from 1990 to 2015. This study included 388 risk-outcome pairs that met World Cancer Research Fund-defined criteria for convincing or probable evidence. We extracted relative risk and exposure estimates from randomised controlled trials, cohorts, pooled cohorts, household surveys, census data, satellite data, and other sources. We used statistical models to pool data, adjust for bias, and incorporate covariates. We developed a metric that allows comparisons of exposure across risk factors—the summary exposure value. Using the counterfactual scenario of theoretical minimum risk level, we estimated the portion of deaths and DALYs that could be attributed to a given risk. We decomposed trends in attributable burden into contributions from population growth, population age structure, risk exposure, and risk-deleted cause-specific DALY rates. We characterised risk exposure in relation to a Socio-demographic Index (SDI). Findings: Between 1990 and 2015, global exposure to unsafe sanitation, household air pollution, childhood underweight, childhood stunting, and smoking each decreased by more than 25%. Global exposure for several occupational risks, high body-mass index (BMI), and drug use increased by more than 25% over the same period. All risks jointly evaluated in 2015 accounted for 57·8% (95% CI 56·6–58·8) of global deaths and 41·2% (39·8–42·8) of DALYs. In 2015, the ten largest contributors to global DALYs among Level 3 risks were high systolic blood pressure (211·8 million [192·7 million to 231·1 million] global DALYs), smoking (148·6 million [134·2 million to 163·1 million]), high fasting plasma glucose (143·1 million [125·1 million to 163·5 million]), high BMI (120·1 million [83·8 million to 158·4 million]), childhood undernutrition (113·3 million [103·9 million to 123·4 million]), ambient particulate matter (103·1 million [90·8 million to 115·1 million]), high total cholesterol (88·7 million [74·6 million to 105·7 million]), household air pollution (85·6 million [66·7 million to 106·1 million]), alcohol use (85·0 million [77·2 million to 93·0 million]), and diets high in sodium (83·0 million [49·3 million to 127·5 million]). From 1990 to 2015, attributable DALYs declined for micronutrient deficiencies, childhood undernutrition, unsafe sanitation and water, and household air pollution; reductions in risk-deleted DALY rates rather than reductions in exposure drove these declines. Rising exposure contributed to notable increases in attributable DALYs from high BMI, high fasting plasma glucose, occupational carcinogens, and drug use. Environmental risks and childhood undernutrition declined steadily with SDI; low physical activity, high BMI, and high fasting plasma glucose increased with SDI. In 119 countries, metabolic risks, such as high BMI and fasting plasma glucose, contributed the most attributable DALYs in 2015. Regionally, smoking still ranked among the leading five risk factors for attributable DALYs in 109 countries; childhood underweight and unsafe sex remained primary drivers of early death and disability in much of sub-Saharan Africa. Interpretation: Declines in some key environmental risks have contributed to declines in critical infectious diseases. Some risks appear to be invariant to SDI. Increasing risks, including high BMI, high fasting plasma glucose, drug use, and some occupational exposures, contribute to rising burden from some conditions, but also provide opportunities for intervention. Some highly preventable risks, such as smoking, remain major causes of attributable DALYs, even as exposure is declining. Public policy makers need to pay attention to the risks that are increasingly major contributors to global burden. Funding: Bill & Melinda Gates Foundation