Clinician-in-the-Loop Annotation of ICU Bedside Alarm Data

In this work, we describe the state of clinical monitoring in the intensive care unit and operating room, where patients are at their most fragile and thus monitoring is most heightened. We describe how large amounts of data generated by monitoring patients’ physiologic signals, along with the ubiquitous aspecific threshold alarms in use today, cause dangerous alarm fatigue for medical caregivers. In order to build more specific, more useful alarms, we gathered a novel data set that would allow us to assess the number, types, and utility of alarms currently in use in the intensive care unit. To do this, we developed a system to collect physiologic monitor data, alarms, and annotations of those alarms provided electronically by clinicians. We describe the collection process for this novel data set and provide a preliminary description of the data

Comparison of questionnaire exposure data to land cover map from geographical information system to assess passive exposure to pesticides: a methodological study

Background: Exposure assessment based on questionnaires is frequently implemented in case-control studies, but possible information and recall bias could lead to misclassification of exposure. Methods: We evaluated passive exposure to pesticides as possible environmental risk factors for amyotrophic lateral scle-rosis (ALS) using a questionnaire mailed to participants in a case-control study in Emilia Romagna and Sicily. Results from questionnaire assessment were com-pared with a remote sensing methodology based on geographical information system, i.e. the land use within a circular 100-meter area around subjects' residence. Since land cover maps were made available only about once every ten years, we used the 2003 and 2009 maps for Emilia-Romagna and Sicily, respectively. Thus, we estimated the percent-age of 'recent' total crop density close to each participant's home, setting positive exposure above 10% of land use. Finally, we calculated the agreement between the two different methodologies using Cohen‟s kappa coefficients for all subjects, cases and controls. Results and Conclusions: Cohen's kappa was 0.364 (95% CI 0.158-0.569) in total population, 0.378 (0.056-0.700) in cases and 0.354 (0.090-0.618) in controls using the most recent land use map available close to year of case diagnosis. Although a moderate-to-low agreement could be seen between two exposure methods, similar results were found in both cases and controls, suggesting that no recall bias occurred in the most recent period. In the future, we plan to compare such agreement using historical residence over the 20-30 years prior to diagnosis, in order to validate the long-term exposure to pesticides in subjects

Expanding phenotype of schimke immuno-osseous dysplasia: Congenital anomalies of the kidneys and of the urinary tract and alteration of nk cells

Schimke immuno-osseous dysplasia (SIOD) is a rare multisystemic disorder with a variable clinical expressivity caused by biallelic variants in SMARCAL1. A phenotype\u2013genotype correlation has been attempted and variable expressivity of biallelic SMARCAL1 variants may be associated with environmental and genetic disturbances of gene expression. We describe two siblings born from consanguineous parents with a diagnosis of SIOD revealed by whole exome sequencing (WES). Results: A homozygous missense variant in the SMARCAL1 gene (c.1682G>A; p.Arg561His) was identified in both patients. Despite carrying the same variant, the two patients showed substantial renal and immunological phenotypic differences. We describe features not previously associated with SIOD\u2014both patients had congenital anomalies of the kidneys and of the urinary tract and one of them succumbed to a classical type congenital mesoblastic nephroma. We performed an extensive characterization of the immunophenotype showing combined immunodeficiency characterized by a profound lymphopenia, lack of thymic output, defective IL-7R\u3b1 expression, and disturbed B plasma cells differentiation and immunoglobulin production in addition to an altered NK-cell phenotype and function. Conclusions: Overall, our results contribute to extending the phenotypic spectrum of features associated with SMARCAL1 mutations and to better characterizing the underlying immunologic disorder with critical implications for therapeutic and management strategies

Perceptions of Cancer Clinical Research Among African American Men in North Carolina

The problem of cancer health disparities is substantial. Clinical trials are widely advocated as a means of reducing disparities and bringing state-of-the-art care to the broader community, where most cancer care is delivered. This study sought to develop a better understanding of why disproportionately few African American men enroll in clinical trials given their substantial cancer burden

Blind trials of computer-assisted structure elucidation software

<p>Abstract</p> <p>Background</p> <p>One of the largest challenges in chemistry today remains that of efficiently mining through vast amounts of data in order to elucidate the chemical structure for an unknown compound. The elucidated candidate compound must be fully consistent with the data and any other competing candidates efficiently eliminated without doubt by using additional data if necessary. It has become increasingly necessary to incorporate an <it>in silico </it>structure generation and verification tool to facilitate this elucidation process. An effective structure elucidation software technology aims to mimic the skills of a human in interpreting the complex nature of spectral data while producing a solution within a reasonable amount of time. This type of software is known as computer-assisted structure elucidation or CASE software. A systematic trial of the ACD/Structure Elucidator CASE software was conducted over an extended period of time by analysing a set of single and double-blind trials submitted by a global audience of scientists. The purpose of the blind trials was to reduce subjective bias. Double-blind trials comprised of data where the candidate compound was unknown to both the submitting scientist and the analyst. The level of expertise of the submitting scientist ranged from novice to expert structure elucidation specialists with experience in pharmaceutical, industrial, government and academic environments.</p> <p>Results</p> <p>Beginning in 2003, and for the following nine years, the algorithms and software technology contained within ACD/Structure Elucidator have been tested against 112 data sets; many of these were unique challenges. Of these challenges 9% were double-blind trials. The results of eighteen of the single-blind trials were investigated in detail and included problems of a diverse nature with many of the specific challenges associated with algorithmic structure elucidation such as deficiency in protons, structure symmetry, a large number of heteroatoms and poor quality spectral data.</p> <p>Conclusion</p> <p>When applied to a complex set of blind trials, ACD/Structure Elucidator was shown to be a very useful tool in advancing the computer's contribution to elucidating a candidate structure from a set of spectral data (NMR and MS) for an unknown. The synergistic interaction between humans and computers can be highly beneficial in terms of less biased approaches to elucidation as well as dramatic improvements in speed and throughput. In those cases where multiple candidate structures exist, ACD/Structure Elucidator is equipped to validate the correct structure and eliminate inconsistent candidates. Full elucidation can generally be performed in less than two hours; this includes the average spectral data processing time and data input.</p

FATTORI AMBIENTALI DI RISCHIO DELLA SCLEROSI LATERALE AMIOTROFICA: UNO STUDIO CASO-CONTROLLO DI POPOLAZIONE BASATO SU QUESTIONARI ANAMNESTICI

Introduzione: La sclerosi laterale amiotrofica (SLA) \ue8 una malattia neurodegenerativa progressiva la cui eziologia \ue8 ancora sostanzialmente ignota, ad eccezione di alcune rare forme di origine genetica. Numerosi suoi possibili fattori di rischio ambientali sono attualmente oggetto di indagine. Metodi: Abbiamo realizzato uno studio caso-controllo di popolazione nelle province di Modena, Reggio Emilia e Catania, al fine di valutare il ruolo eziologico di alcuni possibili fattori ambientali di rischio. Abbiamo somministrato per via postale un questionario finalizzato alla raccolta di informazioni anamnestiche ai casi di SLA diagnosticati nel periodo 2008-2011 e ad un gruppo di controlli di popolazione appaiati per alcune variabili confondenti. Risultati: Il 35% (n=162, 61 casi e 101 controlli) dei questionari inviati \ue8 stato compilato e restituito. In un modello di regressione logistica, i pregressi traumatismi soggetti a valutazione medica sono risultati associati ad un odds ratio (OR) di SLA pari a 1.20 (intervalli di confidenza al 95% (IC 95%) 0.62-2.30), con un valore pi\uf9 elevato (3.04, 1.22-7.55) per traumi alla testa. Gli shock elettrici hanno evidenziato un OR di 2.25 (0.66-7.63). Con riferimento alla storia occupazionale, l\u2019OR associata all\u2019attivit\ue0 lavorativa in ambito agricolo o come saldatore \ue8 risultata rispettivamente pari a 2.44 (1.02-5.79) e 1.25 (0.27-5.80). Aver vissuto in zona agricola \ue8 stato associato ad un lieve aumento del rischio (OR=1.67, 0.87-3.20), a differenza della pratica sportiva e specificatamente del calcio (OR 0.84 (0.46-1.51) e 1.04 (0.44-2.47). Conclusioni: I risultati ottenuti appaiono di potenziale interesse eziologico e meritevoli di ulteriori approfondimenti, pur tenendo conto del rischio di distorsioni di selezione del campione o di informazione, specie nei pazienti

Both SEPT2 and MLL are down-regulated in MLL-SEPT2 therapy-related myeloid neoplasia

<p>Abstract</p> <p>Background</p> <p>A relevant role of septins in leukemogenesis has been uncovered by their involvement as fusion partners in <it>MLL</it>-related leukemia. Recently, we have established the <it>MLL-SEPT2 </it>gene fusion as the molecular abnormality subjacent to the translocation t(2;11)(q37;q23) in therapy-related acute myeloid leukemia. In this work we quantified <it>MLL </it>and <it>SEPT2 </it>gene expression in 58 acute myeloid leukemia patients selected to represent the major AML genetic subgroups, as well as in all three cases of <it>MLL-SEPT2</it>-associated myeloid neoplasms so far described in the literature.</p> <p>Methods</p> <p>Cytogenetics, fluorescence in situ hybridization (FISH) and molecular studies (RT-PCR, qRT-PCR and qMSP) were used to characterize 58 acute myeloid leukemia patients (AML) at diagnosis selected to represent the major AML genetic subgroups: <it>CBFB-MYH11 </it>(n = 13), <it>PML-RARA </it>(n = 12); <it>RUNX1-RUNX1T1 </it>(n = 12), normal karyotype (n = 11), and <it>MLL </it>gene fusions other than <it>MLL-SEPT2 </it>(n = 10). We also studied all three <it>MLL-SEPT2 </it>myeloid neoplasia cases reported in the literature, namely two AML patients and a t-MDS patient.</p> <p>Results</p> <p>When compared with normal controls, we found a 12.8-fold reduction of wild-type <it>SEPT2 </it>and <it>MLL-SEPT2 </it>combined expression in cases with the <it>MLL-SEPT2 </it>gene fusion (p = 0.007), which is accompanied by a 12.4-fold down-regulation of wild-type <it>MLL </it>and <it>MLL-SEPT2 </it>combined expression (p = 0.028). The down-regulation of <it>SEPT2 </it>in <it>MLL-SEPT2 </it>myeloid neoplasias was statistically significant when compared with all other leukemia genetic subgroups (including those with other <it>MLL </it>gene fusions). In addition, <it>MLL </it>expression was also down-regulated in the group of <it>MLL </it>fusions other than <it>MLL-SEPT2</it>, when compared with the normal control group (p = 0.023)</p> <p>Conclusion</p> <p>We found a significant down-regulation of both <it>SEPT2 </it>and <it>MLL </it>in <it>MLL-SEPT2 </it>myeloid neoplasias. In addition, we also found that <it>MLL </it>is under-expressed in AML patients with <it>MLL </it>fusions other than <it>MLL-SEPT2</it>.</p

Fabrication and Repair of Ion Source Components in the 80 keV Neutral Beam Lines for DIII-D

OAK-B135 After 8 years of operation, leaks began to develop in critical components of the ion sources of the 80 keV neutral beam lines in DIII-D. Operational adjustments were made that seemed to remedy the problems, but five years later leaks began occurring again, this time with greater frequency. Failures occurred in the stainless steel bellows and molybdenum rails of the grid rail modules as well as in the Langmuir probes. Failure analyses identified several root causes of the leaks and operational adjustments were again made to mitigate the problems, but the rash of failures depleted the program's supply of spare grid rail modules and probes and removed one of the ion sources from regular operation. Fifteen years after their original fabrication, the ion source components were no longer commercially available. In 2001, a program was initiated to fabricate new grid rail modules, including new molybdenum grid rails, bellows, and stainless steel grid rail holders, as well as new Langmuir probes. In parallel, components removed from service due to leaks were to be repaired with new rails and bellows and returned to service. An overview of the root causes of the service failures is offered, details of the repair processes are described, and a summary and evaluation of the fabrication procedures for the new molybdenum rails, grid modules, and Langmuir probes are given