Informatics for cross-sample analysis with comprehensive two-dimensional gas chromatography and high-resolution mass spectrometry (GCxGC-HRMS)

This paper describes informatics for cross-sample analysis with comprehensive two-dimensional gas chromatography (GCxGC) and high-resolution mass spectrometry (HRMS). GCxGC-HRMS analysis produces large data sets that are rich with information, but highly complex. The size of the data and volume of information requires automated processing for comprehensive cross-sample analysis, but the complexity poses a challenge for developing robust methods. The approach developed here analyzes GCxGC-HRMS data from multiple samples to extract a feature template that comprehensively captures the pattern of peaks detected in the retention-times plane. Then, for each sample chromatogram, the template is geometrically transformed to align with the detected peak pattern and generate a set of feature measurements for cross-sample analyses such as sample classification and biomarker discovery. The approach avoids the intractable problem of comprehensive peak matching by using a few reliable peaks for alignment and peak-based retention-plane windows to define comprehensive features that can be reliably matched for cross-sample analysis. The informatics are demonstrated with a set of 18 samples from breast-cancer tumors, each from different individuals, six each for Grades 1-3. The features allow classification that matches grading by a cancer pathologist with 78% success in leave-one-out cross-validation experiments. The HRMS signatures of the features of interest can be examined for determining elemental compositions and identifying compounds.

Prevalence and predictors of kaposi sarcoma herpes virus seropositivity: a cross-sectional analysis of HIV-infected adults initiating ART in Johannesburg, South Africa

Background Kaposi sarcoma (KS) is the most common AIDS-defining tumour in HIV-infected individuals in Africa. Kaposi sarcoma herpes virus (KSHV) infection precedes development of KS. KSHV co-infection may be associated with worse outcomes in HIV disease and elevated KSHV viral load may be an early marker for advanced HIV disease among untreated patients. We examined the prevalence of KSHV among adults initiating antiretroviral therapy (ART) and compared immunological, demographic and clinical factors between patients seropositive and seronegative for KSHV. Results We analyzed cross-sectional data collected from 404 HIV-infected treatment-naïve adults initiating ART at the Themba Lethu Clinic, Johannesburg, South Africa between November 2008 and March 2009. Subjects were screened at ART initiation for antibodies to KSHV lytic K8.1 and latent Orf73 antigens. Seropositivity to KSHV was defined as positive to either lytic KSHV K8.1 or latent KSHV Orf73 antibodies. KSHV viremia was determined by quantitative PCR and CD3, 4 and 8 lymphocyte counts were determined with flow cytometry. Of the 404 participants, 193 (48%) tested positive for KSHV at ART initiation; with 76 (39%) reactive to lytic K8.1, 35 (18%) to latent Orf73 and 82 (42%) to both. One individual presented with clinical KS at ART initiation. The KSHV infected group was similar to those without KSHV in terms of age, race, gender, ethnicity, smoking and alcohol use. KSHV infected individuals presented with slightly higher median CD3 (817 vs. 726 cells/mm3) and CD4 (90 vs. 80 cells/mm3) counts than KSHV negative subjects. We found no associations between KSHV seropositivity and body mass index, tuberculosis status, WHO stage, HIV RNA levels, full blood count or liver function tests at initiation. Those with detectable KSHV viremia (n = 19), however, appeared to present with signs of more advanced HIV disease including anemia and WHO stage 3 or 4 defining conditions compared to those in whom the virus was undetectable. Conclusions We demonstrate a high prevalence of KSHV among HIV-infected adults initiating ART in a large urban public-sector HIV clinic. KSHV viremia but not KSHV seropositivity may be associated with markers of advanced HIV disease.

A cross-sectional analysis of the prevalence of dental anxiety and its relation to the oral health-related quality of life in patients with dental treatment needs at a university clinic in Switzerland

The aim of this observational, cross-sectional study was to analyse the relationship between dental anxiety (DA) and health-related quality of life aspects associated with oral conditions of a population with dental treatment needs in Switzerland.

Impact of diuretic therapy-associated electrolyte disorders present on admission to the emergency department: a cross-sectional analysis

Diuretics are among the most commonly prescribed medications and, due to their mechanisms of action, electrolyte disorders are common side effects of their use. In the present work we investigated the associations between diuretics being taken and the prevalence of electrolyte disorders on admission as well as the impact of electrolyte disorders on patient outcome.

Non-acute myocardial infarction-related causes of elevated high-sensitive troponin T in the emergency room: a cross-sectional analysis

To systematically investigate putative causes of non-coronary high-sensitive troponin elevations in patients presenting to a tertiary care emergency department. In this cross-sectional analysis, patients who received serial measurements of high-sensitive troponin T between 1 August 2010 and 31 October 2012 at the Department of Emergency Medicine were included. The following putative causes were considered to be associated with non-acute coronary syndrome-related increases in high-sensitive troponin T: acute pulmonary embolism, renal insufficiency, aortic dissection, heart failure, peri-/myocarditis, strenuous exercise, rhabdomyolysis, cardiotoxic chemotherapy, high-frequency ablation therapy, defibrillator shocks, cardiac infiltrative disorders (e.g., amyloidosis), chest trauma, sepsis, shock, exacerbation of chronic obstructive pulmonary disease, and diabetic ketoacidosis. During the study period a total of 1,573 patients received serial measurements of high-sensitive troponin T. Of these, 175 patients were found to have acute coronary syndrome leaving 1,398 patients for inclusion in the study. In 222 (30 %) of patients, no putative cause described in the literature could be attributed to the elevation in high-sensitive troponin T observed. The most commonly encountered mechanism underlying the troponin T elevation was renal insufficiency that was present in 286 patients (57 %), followed by cerebral ischemia in 95 patients (19 %), trauma in 75 patients (15 %) and heart failure in 41 patients (8 %). Non-acute coronary syndrome-associated elevation of high-sensitive troponin T levels is commonly observed in the emergency department. Renal insufficiency and acute cerebral events are the most common conditions associated with high-sensitive troponin T elevation.

Patterns of alcohol and illicit substance use in the United States and Mexico. Substantive and methodologic issues in the cross-national analysis of alcohol and drug use data

This research examines prevalence of alcohol and illicit substance use in the United States and Mexico and associated socio-demographic characteristics. The sources of data for this study are public domain data from the U.S. National Household Survey of Drug Abuse, 1988 (n = 8814), and the Mexican National Survey of Addictions, 1988 (n = 12,579). In addition, this study discusses methodologic issues in cross-cultural and cross-national comparison of behavioral and epidemiologic data from population-based samples. The extent to which patterns of substance abuse vary among subgroups of the U.S. and Mexican populations is assessed, as well as the comparability and equivalence of measures of alcohol and drug use in these national samples.^ The prevalence of alcohol use was somewhat similar in the two countries for all three measures of use: lifetime, past year and past year heavy use, (85.0%, 68.1%, 39.6% and 72.6%, 47.7% and 45.8% for the U.S. and Mexico respectively). The use of illegal substances varied widely between countries, with U.S. respondents reporting significantly higher levels of use than their Mexican counterparts. For example, reported use of any illicit substance in lifetime and past year was 34.2%, 11.6 for the U.S., and 3.3% and 0.6% for Mexico. Despite these differences in prevalence, two demographic characteristics, gender and age, were important correlates of use in both countries. Men in both countries were more likely to report use of alcohol and illicit substances than women. Generally speaking, a greater proportion of respondents in both countries 18 years of age or older reported use of alcohol for all three measures than younger respondents; and a greater proportion of respondents between the ages of 18 and 34 years reported use of illicit substances during lifetime and past year than any other age group.^ Additional substantive research investigating population-based samples and at-risk subgroups is needed to understand the underlying mechanisms of these associations. Further development of cross-culturally meaningful survey methods is warranted to validate comparisons of substance use across countries and societies. ^

Cross-cultural analysis of type D (distressed) personality in 6222 patients with ischemic heart disease: a study from the International HeartQoL Project

BACKGROUND Type D (distressed) personality, the conjoint effect of negative affectivity (NA) and social inhibition (SI), predicts adverse cardiovascular outcomes, and is assessed with the 14-item Type D Scale (DS14). However, potential cross-cultural differences in Type D have not been examined yet in a direct comparison of countries. AIM To examine the cross-cultural validity of the Type D construct and its relation with cardiovascular risk factors, cardiac symptom severity, and depression/anxiety. METHODS In 22 countries, 6222 patients with ischemic heart disease (angina, 33%; myocardial infarction, 37%; or heart failure, 30%) completed the DS14 as part of the International HeartQoL Project. RESULTS Type D personality was assessed reliably across countries (αNA>.80; αSI>.74; except Russia, which was excluded from further analysis). Cross-cultural measurement equivalence was established for Type D personality at all measurement levels, as the factor-item configuration, factor loadings, and error structure were not different across countries (fit: CFI=.91; NFI=.88; RMSEA=.018), as well as across gender and diagnostic subgroups. Type D personality was more prevalent in Southern (37%) and Eastern (35%) European countries compared to Northern (24%) and Western European and English-speaking (both 27%) countries (p<.001). Type D was not confounded by cardiac symptom severity, but was associated with a higher prevalence of hypertension, smoking, sedentary lifestyle, and depression. CONCLUSION Cross-cultural measurement equivalence was demonstrated for the Type D scale in 21 countries. There is a pan-cultural relationship between Type D personality and some cardiovascular risk factors, supporting the role of Type D personality across countries and cardiac conditions.

Electrolyte disorders and in-hospital mortality during prolonged heat periods: a cross-sectional analysis

BACKGROUND Heat periods during recent years were associated with excess hospitalization and mortality rates, especially in the elderly. We intended to study whether prolonged warmth/heat periods are associated with an increased prevalence of disorders of serum sodium and potassium and an increased hospital mortality. METHODS In this cross-sectional analysis all patients admitted to the Department of Emergency Medicine of a large tertiary care facility between January 2009 and December 2010 with measurements of serum sodium were included. Demographic data along with detailed data on diuretic medication, length of hospital stay and hospital mortality were obtained for all patients. Data on daily temperatures (maximum, mean, minimum) and humidity were retrieved by Meteo Swiss. RESULTS A total of 22.239 patients were included in the study. 5 periods with a temperature exceeding 25 °C for 3 to 5 days were noticed and 2 periods with temperatures exceeding 25 °C for more than 5 days were noted. Additionally, 2 periods with 3 to 5 days with daily temperatures exceeding 30 °C were noted during the study period. We found a significantly increased prevalence of hyponatremia during heat periods. However, in the Cox regression analysis, prolonged heat was not associated with the prevalence of disorders of serum sodium or potassium. Admission during a heat period was an independent predictor for hospital mortality. CONCLUSIONS Although we found an increased prevalence of hyponatremia during heat periods, no convincing connection could be found for hypernatremia or disorders of serum potassium.

Reciprocal Relationships between Leader–Member Exchange (LMX) and Job Satisfaction: A Cross‐Lagged Analysis

While previous research has mainly emphasised the importance of leader–member exchange (LMX) to job satisfaction, there is a lack of research on reciprocal relationships between job satisfaction and LMX. In this study, we not only suggest that good LMX increases job satisfaction, but that job satisfaction can also enhance high-quality supervisor–employee relationships. A full cross-lagged panel analysis was used to test reciprocal relationships between LMX and job satisfaction. Employees (N= 279) of a large information technology company filled out questionnaires at two times, with a time lag of 3 months. In line with our predictions, findings revealed a positive relationship between LMX and job satisfaction both at Time 1 and Time 2. Moreover, LMX at Time 1 predicted the increase of job satisfaction at Time 2, and job satisfaction at Time 1 predicted the increase of LMX at Time 2. The results demonstrate the need to consider reciprocal relationships between job satisfaction and LMX when explaining employees' workplace outcomes. Our findings are discussed in terms of positive psychology theory.

Injury severity and mortality of adult zebra crosswalk and non-zebra crosswalk road crossing accidents: a cross-sectional analysis

PRINCIPALS Over a million people worldwide die each year from road traffic injuries and more than 10 million sustain permanent disabilities. Many of these victims are pedestrians. The present retrospective study analyzes the severity and mortality of injuries suffered by adult pedestrians, depending on whether they used a zebra crosswalk. METHODS Our retrospective data analysis covered adult patients admitted to our emergency department (ED) between 1 January 2000 and 31 December 2012 after being hit by a vehicle while crossing the road as a pedestrian. Patients were identified by using a string term. Medical, police and ambulance records were reviewed for data extraction. RESULTS A total of 347 patients were eligible for study inclusion. Two hundred and three (203; 58.5%) patients were on a zebra crosswalk and 144 (41.5%) were not. The mean ISS (injury Severity Score) was 12.1 (SD 14.7, range 1-75). The vehicles were faster in non-zebra crosswalk accidents (47.7 km/n, versus 41.4 km/h, p<0.027). The mean ISS score was higher in patients with non-zebra crosswalk accidents; 14.4 (SD 16.5, range 1-75) versus 10.5 (SD13.14, range 1-75) (p<0.019). Zebra crosswalk accidents were associated with less risk of severe injury (OR 0.61, 95% CI 0.38-0.98, p<0.042). Accidents involving a truck were associated with increased risk of severe injury (OR 3.53, 95%CI 1.21-10.26, p<0.02). CONCLUSION Accidents on zebra crosswalks are more common than those not on zebra crosswalks. The injury severity of non-zebra crosswalk accidents is significantly higher than in patients with zebra crosswalk accidents. Accidents involving large vehicles are associated with increased risk of severe injury. Further prospective studies are needed, with detailed assessment of motor vehicle types and speed.

Towards Faster Method Search Through Static Ecosystem Analysis

Software developers are often unsure of the exact name of the method they need to use to invoke the desired behavior in a given context. This results in a process of searching for the correct method name in documentation, which can be lengthy and distracting to the developer. We can decrease the method search time by enhancing the documentation of a class with the most frequently used methods. Usage frequency data for methods is gathered by analyzing other projects from the same ecosystem - written in the same language and sharing dependencies. We implemented a proof of concept of the approach for Pharo Smalltalk and Java. In Pharo Smalltalk, methods are commonly searched for using a code browser tool called "Nautilus", and in Java using a web browser displaying HTML based documentation - Javadoc. We developed plugins for both browsers and gathered method usage data from open source projects, in order to increase developer productivity by reducing method search time. A small initial evaluation has been conducted showing promising results in improving developer productivity.

Temporal change in prevalence and complications of uveitis associated with juvenile idiopathic arthritis:data from a cross-sectional analysis of a prospective nationwide study

OBJECTIVES To analyse the nationwide prevalence of uveitis in JIA and its complications over a whole decade. METHODS We conducted a prospective, observational and cross-sectional study including all JIA patients from a National Paediatric Rheumatological Database (NPRD) with a uveitis add-on module in Germany (2002-2013). Temporal changes in uveitis prevalence, related secondary complications and anti-inflammatory medication were evaluated. RESULTS A total of 60 centres including 18,555 JIA patients (mean 3,863 patients/year, SD=837) were documented in the NPRD between 2002 and 2013. The mean age of the patients was 11.4±4.6 years, their mean disease duration 4.4±3.7 years. Among them, 66.9% were female and 51.7% ANA positive. Patients' mean age at arthritis onset was 6.9±4.5 years. Treatment rates with synthetic and biological DMARDs increased during the observation period (sDMARD: 39.8% to 47.2%, bDMARD: 3.3% to 21.8%). Uveitis prevalence decreased significantly from 2002 to 2013 (13.0% to 11.6%, OR = 0.98, p=0.015). The prevalence of secondary uveitis complications also decreased significantly between 2002 and 2013 (33.6% to 23.9%, OR=0.94, p<0.001). Among the complications, the most common ones were posterior synechiae, cataract and band keratopathy. A significant increase in achieving uveitis inactivity was observed at 30.6% in 2002 and 65.3% in 2013 (OR=1.15, p<0.001). CONCLUSIONS Uveitis prevalence and complications significantly decreased between 2002 and 2013. This may be associated with a more frequent use of DMARDs.

Post-colonial (American?) English Presence on the North-Western Pacific Island of Kosrae: A cross-linguistic analysis of the overlaps and divergences of Kosraean English compared to standard American English

Kosrae is the most remote island of the Federated States of Micronesia (FSM), with a population of less than 7,000 inhabitants, located in the Pacific Ocean between Hawaii and Guam. FSM is an independent sovereign nation consisting of four states in total: Pohnpei, Chuuk, Yap, and Kosrae. Having passed through the hands of Spain, Germany and Japan, the United States gained administrative control of FSM after WWII, as commissioned by the UN. The FSM became an independent nation in 1986 while still retaining affiliation with the US under a ‘Compact of Free Association’. Now both Kosraean and English are considered to be the two official languages and the variety of Kosraean English which has arisen proves for an interesting comparative study. In order to obtain the relevant data, I spent three months on the island of Kosrae, interviewing 90 local speakers, ranging in age (16-70), occupation, sex and time spent off island. The 45 minute long interviews were informal but supported by participant information to capture relevant data and conversations were guided in a way that aimed to reveal language and cultural attitudes. With reference to these samples, I examine the effects of American English on the language use in Kosrae. This paper aims to present a broad analysis of phonological, morphosyntactic and pragmatic features, such as pro-dropping, discourse markers and other practices in order to demonstrate the similarities and differences between the two varieties, which are coming to shape the variety developing on Kosrae. Having transcribed conversations using the tool Elan, I will put particular focus on [h] deletion and insertion, a rare occurrence found in a variety of post-colonial American English which I believe is of particular interest. I assess the presence of English in Kosrae with reference to sociological influences, past and present. First, I discuss the extralinguistic factors which have shaped the English that is currently used on Kosrae, including migration between US and FSM, and English as a language of administration, social media usage and visual media presence. Secondly, I assess the use of English in this community in light of Schneider’s (2007) ‘Dynamic Model’, with reference to America’s contribution as an ‘exploitation colony’ as defined by Mufwene (2001). Finally, an overview of the salient linguistic characteristics of Kosraean English, based on the data collected will be presented and compared to features associated with standard American English in view of examining overlap and divergence. The overall objective is to present a cross-linguistic description of a hitherto unexamined English emerging in a postcolonial environment with a juxtaposed contact variety. Mufwene, Salikoko S. 2001. The ecology of language evolution. Cambridge: Cambridge University Press. Schneider, E. (2007). Postcolonial Englishes. Cambridge: Cambridge University Press. Segal, H.G. (1989) Kosrae, The Sleeping Lady Awakens. Kosrae: Kosrae Tourist Division, Dept. Of Conservation and Development. Keywords: American English, Global English, Pacific English, Morphosyntactic, Phonological, Variation, Discourse