Pre-operative localization of solitary pulmonary nodules with computed tomography-guided hook wire: report of 181 patients.

BACKGROUND: Video-assisted thoracic surgery (VATS) is currently performed to diagnose and treat solitary pulmonary nodules (SPN). However, the intra-operative identification of deep nodules can be challenging with VATS as the lung is difficult to palpate. The aim of the study was to report the utility and the results of pre-operative computed tomography (CT)-guided hook wire localization of SPN. METHODS: All records of the patients undergoing CT-guided hook wire localization prior to VATS resection for SPN between 2002 and 2013 were reviewed. The efficacy in localizing the nodule, hook wire complications, necessity to convert VATS to thoracotomy and the histology of SPN are reported. RESULTS: One hundred eighty-one patients (90 females, mean age 63 y, range 28-82 y) underwent 187 pulmonary resections after CT-guided hook wire localization. The mean SPN diameter was 10.3 mm (range: 4-29 mm). The mean distance of the lesion from the pleural surface was 11.6 mm (range: 0-45 mm). The mean time interval from hook wire insertion to VATS resection was 224 min (range 54-622 min). Hook wire complications included pneumothorax requiring chest tube drainage in 4 patients (2.1%) and mild parenchymal haemorrhage in 11 (5.9%) patients. Migration of the hook wire occurred in 7 patients (3.7%) although it did not affect the success of VATS resection (nodule location guided by the lung puncture site). Three patients underwent additional wedge resection by VATS during the same procedure because no lesion was identified in the surgical specimen. Conversion thoracotomy was required in 13 patients (7 %) for centrally localized lesions (6 patients) and pleural adhesions (7 patients). The mean operative time was 60 min (range 18-135 min). Pathological examination revealed a malignant lesion in 107 patients (59 %). The diagnostic yield was 98.3 %. CONCLUSION: VATS resection for SPN after CT-guided hook wire localization for SPN is safe and allows for proper diagnosis with a low thoracotomy conversion rate

Vedolizumab for Treating Moderately to Severely Active Crohn’s Disease After Prior Therapy: An Evidence Review Group Perspective of a NICE Single Technology Appraisal

As part of its single technology appraisal process, the National Institute for Health and Care Excellence (NICE) invited the manufacturer of vedolizumab (Takeda UK) to submit evidence of the clinical effectiveness and cost effectiveness of vedolizumab for the treatment of patients with moderate-to-severe, active Crohn’s disease. The School of Health and Related Research (ScHARR) at the University of Sheffield was commissioned as the Evidence Review Group (ERG) and produced a critical review of the evidence of the clinical effectiveness and cost effectiveness of the technology, based upon the company’s submission to NICE. The GEMINI II and III trials formed the main supporting evidence for the intervention. Both studies were phase III, randomised, double-blind, placebo-controlled, multicentre trials designed to evaluate the efficacy and safety of vedolizumab. They included patients who were naïve to tumour necrosis factor alpha antagonist (anti-TNF-α) therapy and patients who had an inadequate response to, loss of response to or intolerance of immunomodulators or anti-TNF-α agents. GEMINI II was designed to evaluate the efficacy and safety of vedolizumab as an induction treatment (dosing at weeks 0 and 2, with assessment at week 6) and maintenance treatment (during weeks 6–52). In contrast, GEMINI III was designed to evaluate the efficacy and safety of vedolizumab as an induction treatment only, with doses at weeks 0, 2 and 6, and assessment at weeks 6 and 10. In the absence of any direct head-to-head, randomised, controlled trials comparing vedolizumab with other relevant biologic therapies (adalimumab and infliximab) for the treatment of moderate-to-severe Crohn’s disease, the company conducted a network meta-analysis, which compared vedolizumab, adalimumab, infliximab and placebo for the outcomes of clinical response, enhanced clinical response, clinical remission and discontinuation due to adverse events. The company model estimated the incremental cost-effectiveness ratio (ICER) for vedolizumab compared with the standard of care (consisting of 5-aminosalicylic acids, corticosteroids and immunosuppressants) to be £21,620 per quality-adjusted life-year (QALY) gained within the anti-TNF-α-failure population (which included a confidential patient access scheme for vedolizumab). The ICERs were above £30,000 per QALY gained for the mixed intention-to-treat population (including both anti-TNF-α-naïve and anti-TNF-α-failure populations) and in patients who were anti-TNF-α naïve only. The ERG identified a number of limitations that were believed to limit the robustness of the results presented by the company. These limitations could not be addressed by the ERG without major restructuring of the economic model. Therefore, the ERG concluded that the results from the company’s model needed to be interpreted with caution and that it was unclear whether the ICERs would increase or decrease following amendment of the identified structural issues

Essays on the Evaluation of Environmental Programs

This dissertation comprises four chapters. The unifying theme is the evaluation of environmental programs. Specifically, each chapter examines some facet of the impacts of protected areas. The first chapter examines the heterogeneous environmental and economic impacts of protected areas in Costa Rica. Previous studies suggest that Costa Rica\u27s protected area system induced both reduced deforestation and alleviated poverty. We demonstrate that these environmental and social impacts were spatially heterogeneous. Importantly, the characteristics associated with the most avoided deforestation are the characteristics associated with the least poverty alleviation. In other words, the same characteristics that have limited the conservation effectiveness of protected areas may have improved the social welfare impacts of these areas. These results suggest that `win-win\u27 efforts to protect ecosystems and alleviate poverty may be possible when policymakers are satisfied with low levels of each outcome, but tradeoffs exist when more of either outcome is desired. The second chapter explores in more detail the heterogeneous impacts of protected areas in Costa Rica and Thailand. In particular we investigate the potential for protected areas to act as a mechanism for poverty traps and use semiparametric models to identify the spatial congruence of environmental and economic outcomes. We find no evidence that protected areas trap historically poorer areas in poverty. In fact, we find that poorer areas at baseline appear to have the greatest levels of poverty reduction as a result of protection. However, we do find that the spatial characteristics associated with the most poverty alleviation are not necessarily the characteristics associated with the most avoided deforestation. We demonstrate how an understanding of these spatially heterogeneous responses to protection can be used to generate suitability maps that identify locations in which both environmental and poverty alleviation goals are most likely to be achieved. In the third chapter we address the mechanisms through which protected areas affect economic outcomes. Using recently developed quasi-experimental methods and rich biophysical and demographic data, we quantify the causal post-treatment mechanism impacts of tourism, infrastructure development and ecosystem services on poverty, due to the establishment of protected areas in Costa Rica prior to 1980. We find that nearly 50% of the poverty reduction estimated in a previous study can be attributed to tourism. In addition, although the mechanism estimates for the infrastructure and ecosystem services proxies are negligible, we argue that the results provide evidence that enhanced ecosystem services from the establishment of protected areas has likely helped to reduce poverty. The results provide additional information to policy makers that wish to enhance the future establishment of protected areas with complementary policy. The final chapter studies the economic impacts of protected areas in Bolivia. We find that municipalities with at least 10% of their area occupied by a protected area between 1992 and 2000 exhibited differentially greater levels of poverty reduction between 1992 and 2001 compared to similar municipalities unaffected by protected areas. We find that the results are robust to a number of econometric specifications, spillover analyses and a placebo study. Although the overarching results that Bolivia\u27s protected areas were associated with poverty reduction are similar to previous studies , the underlying results are subtly, but significantly, different. In previous studies it was found that controlling for key observable covariates lead to fundamentally antithetical results compared to naive estimates. Conversely, these results indicate that naive estimates lead to an over-estimation of the poverty reducing impacts of protected areas. The results expose the heterogeneity of protected area impacts across countries and, therefore, underscore the importance of country-level impact evaluations in order to build the global knowledge base regarding the socioeconomic impacts of protected areas

Deletion of the Coffin-Lowry Syndrome Gene Rsk2 in Mice is Associated With Impaired Spatial Learning and Reduced Control of Exploratory Behavior

Coffin-Lowry Syndrome (CLS) is an X-linked syndromic form of mental retardation associated with skeletal abnormalities. It is caused by mutations of the Rsk2 gene, which encodes a growth factor regulated kinase. Gene deletion studies in mice have shown an essential role for the Rsk2 gene in osteoblast differentiation and function, establishing a causal link between Rsk2 deficiency and skeletal abnormalities of CLS. Although analyses in mice have revealed prominent expression of Rsk2 in brain structures that are essential for learning and memory, evidence at the behavioral level for an involvement of Rsk2 in cognitive function is still lacking. Here, we have examined Rsk2-deficient mice in two extensive batteries of behavioral tests, which were conducted independently in two laboratories in Zurich (Switzerland) and Orsay (France). Despite the known reduction of bone mass, all parameters of motor function were normal, confirming the suitability of Rsk2-deficient mice for behavioral testing. Rsk2-deficient mice showed a mild impairment of spatial working memory, delayed acquisition of a spatial reference memory task and long-term spatial memory deficits. In contrast, associative and recognition memory, as well as the habituation of exploratory activity were normal. Our studies also revealed mild signs of disinhibition in exploratory activity, as well as a difficulty to adapt to new test environments, which likely contributed to the learning impairments displayed by Rsk2-deficient mice. The observed behavioral changes are in line with observations made in other mouse models of human mental retardation and support a role of Rsk2 in cognitive function

Correct quantum chemistry in a minimal basis from effective Hamiltonians

We describe how to create ab-initio effective Hamiltonians that qualitatively describe correct chemistry even when used with a minimal basis. The Hamiltonians are obtained by folding correlation down from a large parent basis into a small, or minimal, target basis, using the machinery of canonical transformations. We demonstrate the quality of these effective Hamiltonians to correctly capture a wide range of excited states in water, nitrogen, and ethylene, and to describe ground and excited state bond-breaking in nitrogen and the chromium dimer, all in small or minimal basis sets

Baseline body mass index among children and adults undergoing allogeneic hematopoietic cell transplantation: clinical characteristics and outcomes

Obesity is an important public health problem that may influence the outcomes of hematopoietic cell transplantation (HCT). We studied 898 children and adults receiving first-time allogeneic hematopoietic stem cell transplants between 2004 and 2012. Pre-transplant body mass index (BMI) was classified as underweight, normal weight, overweight, or obese using the WHO classification, or age-adjusted BMI percentiles for children. The study population was predominantly Caucasian, and the median age was 51 years (5 months – 73 years). The cumulative 3-year incidence of non-relapse mortality (NRM) in underweight, normal weight, overweight, and obese patients was 20%, 19%, 20%, and 33%, respectively. Major causes of NRM were acute and chronic graft-versus-host disease (GVHD). The corresponding incidence of relapse was 30%, 41%, 37%, and 30%, respectively. Three-year overall survival was 59%, 48%, 47%, and 43%, respectively. Multivariate analysis showed that obesity was associated with higher NRM (HR 1.43, p=0.04), and lower relapse (HR 0.65, p=0.002). Pre-transplant plasma levels of ST2 and TNFR1 biomarkers were significantly higher in obese compared with normal weight patients (p=0.04 and p=0.05, respectively). The increase in NRM observed in obese patients was partially offset by lower incidence of relapse with no difference in overall survival

PubMed QUEST: The PubMed Query Search Tool. An informatics tool to aid cancer centers and cancer investigators in searching the PubMed databases

Searching PubMed for citations related to a specific cancer center or group of authors can be labor-intensive. We have created a tool, PubMed QUEST, to aid in the rapid searching of PubMed for publications of interest. It was designed by taking into account the needs of entire cancer centers as well as individual investigators. The experience of using the tool by our institution’s cancer center administration and investigators has been favorable and we believe it could easily be adapted to other institutions. Use of the tool has identified limitations of automated searches for publications based on an author’s name, especially for common names. These limitations could likely be solved if the PubMed database assigned a unique identifier to each author

Gerstmann-Straussler-Scheinker disease in an Alsatian family: clinical and genetic studies

The clinical progression of Gerstmann-Straussler-Scheinker disease in a family of Alsatian origin is reported. The age of onset and the duration of evolution were variable. The clinical picture became more complex over the generations: in the first generations, isolated dementia and in later generations a triad of pyramidal, pseudobulbar syndromes and dementia associated with spinal cord and cerebellar features. Prion gene analysis showed that four surviving patients carry double missense changes at codons 117 and 129, identical to those found in one case at necropsy and 10 other healthy members of the family. The missense changes were not found in 100 controls. No member of the family had modification of condons 102, 178, or 200. The lod score suggests linkage between the missense change at codon 117 and Gerstmann- Straussler-Scheinker disease in this family

Clinical narrative analytics challenges

Precision medicine or evidence based medicine is based on the extraction of knowledge from medical records to provide individuals with the appropriate treatment in the appropriate moment according to the patient features. Despite the efforts of using clinical narratives for clinical decision support, many challenges have to be faced still today such as multilinguarity, diversity of terms and formats in different services, acronyms, negation, to name but a few. The same problems exist when one wants to analyze narratives in literature whose analysis would provide physicians and researchers with highlights. In this talk we will analyze challenges, solutions and open problems and will analyze several frameworks and tools that are able to perform NLP over free text to extract medical entities by means of Named Entity Recognition process. We will also analyze a framework we have developed to extract and validate medical terms. In particular we present two uses cases: (i) medical entities extraction of a set of infectious diseases description texts provided by MedlinePlus and (ii) scales of stroke identification in clinical narratives written in Spanish

Estimating the Impacts of Bolivia\u27s Protected Areas on Poverty

Protected areas represent a powerful policy tool for the preservation of ecosystems and their services. The rapid proliferation of protected areas in Bolivia over the past several decades has prompted interest in understanding their impacts on surrounding populations. Recent studies from other developing countries show that protected areas have had positive impacts on poverty. Using rich biophysical and socioeconomic data from Bolivia we and that municipalities with at least 10% of their area occupied by a protected area established between 1992 and 2000 exhibited differentially greater levels of poverty reduction between 1992 and 2001 compared to similar municipalities indicted by protected areas. We and that our results are robust to a number of econometric specifications, spillover analyses and a placebo study. Although our overarching results that Bolivia\u27s protected areas were associated with poverty reduction are similar to previous studies, our underlying results di are subtly, but significantly. Previous studies found that controlling for key observable covariates led to fundamentally antithetical results compared to na+ye (uncontrolled) estimates. Conversely, our results indicate that na+ve estimates lead to an over estimation of the poverty reducing impacts of protected areas. Our results expose the heterogeneity of protected area impacts across countries and, therefore, underscore the importance of country-level impact evaluations in order to build the global knowledge base regarding the socioeconomic impacts of protected areas