Dynamics of a minimal model of interlocked positive and negative feedback loops of transcriptional regulation by cAMP-response element binding proteins.

cAMP-response element binding (CREB) proteins are involved in transcriptional regulation in a number of cellular processes (e.g., neural plasticity and circadian rhythms). The CREB family contains activators and repressors that may interact through positive and negative feedback loops. These loops can be generated by auto- and cross-regulation of expression of CREB proteins, via CRE elements in or near their genes. Experiments suggest that such feedback loops may operate in several systems (e.g., Aplysia and rat). To understand the functional implications of such feedback loops, which are interlocked via cross-regulation of transcription, a minimal model with a positive and negative loop was developed and investigated using bifurcation analysis. Bifurcation analysis revealed diverse nonlinear dynamics (e.g., bistability and oscillations). The stability of steady states or oscillations could be changed by time delays in the synthesis of the activator (CREB1) or the repressor (CREB2). Investigation of stochastic fluctuations due to small numbers of molecules of CREB1 and CREB2 revealed a bimodal distribution of CREB molecules in the bistability region. The robustness of the stable HIGH and LOW states of CREB expression to stochastic noise differs, and a critical number of molecules was required to sustain the HIGH state for days or longer. Increasing positive feedback or decreasing negative feedback also increased the lifetime of the HIGH state, and persistence of this state may correlate with long-term memory formation. A critical number of molecules was also required to sustain robust oscillations of CREB expression. If a steady state was near a deterministic Hopf bifurcation point, stochastic resonance could induce oscillations. This comparative analysis of deterministic and stochastic dynamics not only provides insights into the possible dynamics of CREB regulatory motifs, but also demonstrates a framework for understanding other regulatory processes with similar network architecture.

Ambulatory care adverse events and preventable adverse events leading to a hospital admission.

BACKGROUND: Most healthcare in the US is delivered in the ambulatory care setting, but the epidemiology of errors and adverse events in ambulatory care is understudied. METHODS: Using the population-based data from the Colorado and Utah Medical Practices Study, we identified adverse events that occurred in an ambulatory care setting and led to hospital admission. Proportions with 95% CIs are reported. RESULTS: We reviewed 14,700-hospital discharge records and found 587 adverse events of which 70 were ambulatory care adverse events (AAEs) and 31 were ambulatory care preventable adverse events (APAEs). When weighted to the general population, there were 2608 AAEs and 1296 (44.3%) APAEs in Colorado and Utah, USA, in 1992. APAEs occurred most commonly in physicians' offices (43.1%, range 46.8-27.8), the emergency department (32.3%, 46.1-18.5) and at home (13.1%, 23.1-3.1). APAEs in day surgery were less common (7.1%, 13.6-0.6) but caused the greatest harm to patients. The types of APAEs were broadly distributed among missed or delayed diagnoses (36%, 50.2-21.8), surgery (24.1%, 36.7-11.5), non-surgical procedures (14.6%, 25.0-4.2), medication (13.1%, 23.1-3.1) and therapeutic events (12.3%, 22.0-2.6). Overall, 10% of the APAEs resulted in serious permanent injury or death. The proportion of APAEs that resulted in death was 31.8% for general internal medicine, 22.5% for family practice and 16.7% for emergency medicine. CONCLUSION: An estimated 75,000 hospitalisations per year are due to preventable adverse events that occur in outpatient settings in the US, resulting in 4839 serious permanent injuries and 2587 deaths.

Time-kill and synergism studies of ceftobiprole against Enterococcus faecalis, including beta-lactamase-producing and vancomycin-resistant isolates.

Ceftobiprole (BAL9141) is an investigational cephalosporin with broad in vitro activity against gram-positive cocci, including enterococci. Ceftobiprole MICs were determined for 93 isolates of Enterococcus faecalis (including 16 beta-lactamase [Bla] producers and 17 vancomycin-resistant isolates) by an agar dilution method following the Clinical and Laboratory Standards Institute recommendations. Ceftobiprole MICs were also determined with a high inoculum concentration (10(7) CFU/ml) for a subset of five Bla producers belonging to different previously characterized clones by a broth dilution method. Time-kill and synergism studies (with either streptomycin or gentamicin) were performed with two beta-lactamase-producing isolates (TX0630 and TX5070) and two vancomycin-resistant isolates (TX2484 [VanB] and TX2784 [VanA]). The MICs of ceftobiprole for 50 and 90% of the isolates tested were 0.25 and 1 microg/ml, respectively. All Bla producers and vancomycin-resistant isolates were inhibited by concentrations of

Western diet, but not high fat diet, causes derangements of fatty acid metabolism and contractile dysfunction in the heart of Wistar rats.

Obesity and diabetes are associated with increased fatty acid availability in excess of muscle fatty acid oxidation capacity. This mismatch is implicated in the pathogenesis of cardiac contractile dysfunction and also in the development of skeletal-muscle insulin resistance. We tested the hypothesis that 'Western' and high fat diets differentially cause maladaptation of cardiac- and skeletal-muscle fatty acid oxidation, resulting in cardiac contractile dysfunction. Wistar rats were fed on low fat, 'Western' or high fat (10, 45 or 60% calories from fat respectively) diet for acute (1 day to 1 week), short (4-8 weeks), intermediate (16-24 weeks) or long (32-48 weeks) term. Oleate oxidation in heart muscle ex vivo increased with high fat diet at all time points investigated. In contrast, cardiac oleate oxidation increased with Western diet in the acute, short and intermediate term, but not in the long term. Consistent with fatty acid oxidation maladaptation, cardiac power decreased with long-term Western diet only. In contrast, soleus muscle oleate oxidation (ex vivo) increased only in the acute and short term with either Western or high fat feeding. Fatty acid-responsive genes, including PDHK4 (pyruvate dehydrogenase kinase 4) and CTE1 (cytosolic thioesterase 1), increased in heart and soleus muscle to a greater extent with feeding a high fat diet compared with a Western diet. In conclusion, we implicate inadequate induction of a cassette of fatty acid-responsive genes, and impaired activation of fatty acid oxidation, in the development of cardiac dysfunction with Western diet.

Computational identification and functional validation of regulatory motifs in cartilage-expressed genes.

Chondrocyte gene regulation is important for the generation and maintenance of cartilage tissues. Several regulatory factors have been identified that play a role in chondrogenesis, including the positive transacting factors of the SOX family such as SOX9, SOX5, and SOX6, as well as negative transacting factors such as C/EBP and delta EF1. However, a complete understanding of the intricate regulatory network that governs the tissue-specific expression of cartilage genes is not yet available. We have taken a computational approach to identify cis-regulatory, transcription factor (TF) binding motifs in a set of cartilage characteristic genes to better define the transcriptional regulatory networks that regulate chondrogenesis. Our computational methods have identified several TFs, whose binding profiles are available in the TRANSFAC database, as important to chondrogenesis. In addition, a cartilage-specific SOX-binding profile was constructed and used to identify both known, and novel, functional paired SOX-binding motifs in chondrocyte genes. Using DNA pattern-recognition algorithms, we have also identified cis-regulatory elements for unknown TFs. We have validated our computational predictions through mutational analyses in cell transfection experiments. One novel regulatory motif, N1, found at high frequency in the COL2A1 promoter, was found to bind to chondrocyte nuclear proteins. Mutational analyses suggest that this motif binds a repressive factor that regulates basal levels of the COL2A1 promoter.

The relationship between the field-shifting phenomenon and representational coherence of place cells in CA1 and CA3 in a cue-altered environment.

Subfields of the hippocampus display differential dynamics in processing a spatial environment, especially when changes are introduced to the environment. Specifically, when familiar cues in the environment are spatially rearranged, place cells in the CA3 subfield tend to rotate with a particular set of cues (e.g., proximal cues), maintaining a coherent spatial representation. Place cells in CA1, in contrast, display discordant behaviors (e.g., rotating with different sets of cues or remapping) in the same condition. In addition, on average, CA3 place cells shift their firing locations (measured by the center of mass, or COM) backward over time when the animal encounters the changed environment for the first time, but not after that first experience. However, CA1 displays an opposite pattern, in which place cells exhibit the backward COM-shift only from the second day of experience, but not on the first day. Here, we examined the relationship between the environment-representing behavior (i.e., rotation vs. remapping) and the COM-shift of place fields in CA1 and CA3. Both in CA1 and CA3, the backward (as well as forward) COM-shift phenomena occurred regardless of the rotating versus remapping of the place cell. The differential, daily time course of the onset/offset of backward COM-shift in the cue-altered environment in CA1 and CA3 (on day 1 in CA1 and from day 2 onward in CA3) stems from different population dynamics between the subfields. The results suggest that heterogeneous, complex plasticity mechanisms underlie the environment-representating behavior (i.e., rotate/remap) and the COM-shifting behavior of the place cell.

Severe aortic and arterial aneurysms associated with a TGFBR2 mutation.

BACKGROUND: A 24-year-old man presented with previously diagnosed Marfan's syndrome. Since the age of 9 years, he had undergone eight cardiovascular procedures to treat rapidly progressive aneurysms, dissection and tortuous vascular disease involving the aortic root and arch, the thoracoabdominal aorta, and brachiocephalic, vertebral, internal thoracic and superior mesenteric arteries. Throughout this extensive series of cardiovascular surgical repairs, he recovered without stroke, paraplegia or renal impairment. INVESTIGATIONS: CT scans, arteriogram, genetic mutation screening of transforming growth factor beta receptors 1 and 2. DIAGNOSIS: Diffuse and rapidly progressing vascular disease in a patient who met the diagnostic criteria for Marfan's syndrome, but was later rediagnosed with Loeys-Dietz syndrome. Genetic testing also revealed a de novo mutation in transforming growth factor beta receptor 2. MANAGEMENT: Regular cardiovascular surveillance for aneurysms and dissections, and aggressive surgical treatment of vascular disease.

Strengthening the Reporting of Observational Studies in Epidemiology (STROBE): Explanation and elaboration

Much medical research is observational. The reporting of observational studies is often of insufficient quality. Poor reporting hampers the assessment of the strengths and weaknesses of a study and the generalisability of its results. Taking into account empirical evidence and theoretical considerations, a group of methodologists, researchers, and editors developed the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) recommendations to improve the quality of reporting of observational studies. The STROBE Statement consists of a checklist of 22 items, which relate to the title, abstract, introduction, methods, results and discussion sections of articles. Eighteen items are common to cohort studies, case-control studies and cross-sectional studies and four are specific to each of the three study designs. The STROBE Statement provides guidance to authors about how to improve the reporting of observational studies and facilitates critical appraisal and interpretation of studies by reviewers, journal editors and readers. This explanatory and elaboration document is intended to enhance the use, understanding, and dissemination of the STROBE Statement. The meaning and rationale for each checklist item are presented. For each item, one or several published examples and, where possible, references to relevant empirical studies and methodological literature are provided. Examples of useful flow diagrams are also included. The STROBE Statement, this document, and the associated Web site (http://www.strobe-statement.org/) should be helpful resources to improve reporting of observational research.

High Incorrect Use of the Standard Error of the Mean (SEM) in Original Articles in Three Cardiovascular Journals Evaluated for 2012.

RATIONALE In biomedical journals authors sometimes use the standard error of the mean (SEM) for data description, which has been called inappropriate or incorrect. OBJECTIVE To assess the frequency of incorrect use of SEM in articles in three selected cardiovascular journals. METHODS AND RESULTS All original journal articles published in 2012 in Cardiovascular Research, Circulation: Heart Failure and Circulation Research were assessed by two assessors for inappropriate use of SEM when providing descriptive information of empirical data. We also assessed whether the authors state in the methods section that the SEM will be used for data description. Of 441 articles included in this survey, 64% (282 articles) contained at least one instance of incorrect use of the SEM, with two journals having a prevalence above 70% and "Circulation: Heart Failure" having the lowest value (27%). In 81% of articles with incorrect use of SEM, the authors had explicitly stated that they use the SEM for data description and in 89% SEM bars were also used instead of 95% confidence intervals. Basic science studies had a 7.4-fold higher level of inappropriate SEM use (74%) than clinical studies (10%). LIMITATIONS The selection of the three cardiovascular journals was based on a subjective initial impression of observing inappropriate SEM use. The observed results are not representative for all cardiovascular journals. CONCLUSION In three selected cardiovascular journals we found a high level of inappropriate SEM use and explicit methods statements to use it for data description, especially in basic science studies. To improve on this situation, these and other journals should provide clear instructions to authors on how to report descriptive information of empirical data.

Changes in serum lipids with change and fluctuation in body mass index and body fat distribution in Mexican Americans with type 2 diabetes

This dissertation was written in the format of three journal articles. Paper 1 examined the influence of change and fluctuation in body mass index (BMI) over an eleven-year period, on changes in serum lipid levels (total, HDL, and LDL cholesterol, triglyceride) in a population of Mexican Americans with type 2 diabetes. Linear regression models containing initial lipid value, BMI and age, BMI change (slope of BMI), and BMI fluctuation (root mean square error) were used to investigate associations of these variables with change in lipids over time. Increasing BMI over time was associated with gains in total and LDL cholesterol and triglyceride levels in women. Fluctuation of BMI was not associated with detrimental lipid profiles. These effects were independent of age and were not statistically significant in men. In Mexican-American women with type 2 diabetes, weight reduction is likely to result in more favorable levels of total and LDL cholesterol and triglyceride, without concern for possible detrimental effects of weight fluctuation. Weight reduction may not be as effective in men, but does not appear to be harmful either. ^ Paper 2 examined the associations of upper and total body fat with total cholesterol, HDL and LDL cholesterol, and triglyceride levels in the same population. Multilevel analysis was used to predict serum lipid levels from total body fat (BMI and triceps skinfold) and upper body fat (subscapular skinfold), while controlling for the effects of sex, age and self-correlations across time. Body fat was not strikingly associated with trends in serum lipid levels. However, upper body fat was strongly associated with triglyceride levels. This suggests that loss of upper body fat may be more important than weight loss in management of the hypertriglyceridemia commonly seen in type 2 diabetes. ^ Paper 3 was a review of the literature reporting associations between weight fluctuation and lipid levels. Few studies have reported associations between weight fluctuation and total, LDL, and HDL cholesterol and triglyceride levels. The body of evidence to date suggests that weight fluctuation does not strongly influence levels of total, LDL and HDL cholesterol and triglyceride. ^

Use of intranet and other interventions to increase influenza vaccination among health care workers

Influenza (the flu) is a serious respiratory illness that can cause severe complications, often leading to hospitalization and even death. Influenza epidemics occur in most countries every year, usually during the winter months. Despite recommendations from the Centers for Disease Control and Prevention (CDC) and efforts by health care institutions across the United States, influenza vaccination rates among health care workers in the United States remain low. How to increase the number of vaccinated health care workers is an important public health question and is examined in two journal articles included here. ^ The first journal article evaluates the effectiveness of an Intranet intervention in increasing the proportion of health care workers (HCWs) who received influenza vaccination. Hospital employees were required go to the hospital's Intranet and select "vaccine received," "contraindicated," or "declined" from the online questionnaire. Declining employees automatically received an online pop-up window with education about vaccination; managers were provided feedback on employees' participation rates via e-mail messages. Employees were reminded of the Intranet requirement in articles in the employee newsletter and on the hospital's Intranet. Reminders about the Intranet questionnaire were provided through managers and newsletters to the HCWs. Fewer than half the employees (43.7%) completed the online questionnaire. Yet the hospital witnessed a statistically significant increase in the percentage of employees who received the flu vaccine at the hospital – 48.5% in the 2008-09 season as compared to 36.5%, 38.5% and 29.8% in the previous three years (P < 0.05). ^ The second article assesses current interventions employed by hospitals, health systems and nursing homes to determine which policies have been the most effective in boosting vaccination rates among American health care workers. A systematic review of research published between January 1994 and March 2010 suggests that education is necessary but not usually sufficient to increase vaccine uptake. Education about the flu and flu vaccines is most effective when complemented with easy access and making the vaccine free, although this combination may not be sufficient to achieve the desired vaccination levels among HCWs. The findings point toward adding incentives for HCWs to get vaccinated and requiring them to record their vaccination status on a declination/consent form – either written or electronic. ^ Based on these findings, American health care organizations, such as hospitals, nursing homes, and long-term care facilities, should consider using online declination forms as a method for increasing influenza vaccination rates among their employees. These online forms should be used in conjunction with other policies, including free vaccine, mobile distribution and incentives. ^ To further spur health care organizations to adopt policies and practices that will raise influenza vaccination rates among employees, The Joint Commission – an independent, not-for- profit organization that accredits and certifies more than 17,000 health care organizations and programs in the United States – should consider altering its standards. Currently, The Joint Commission does not require signed declination forms from employees who eschew vaccination; it only echoes the CDC's recommendations: "Health care facilities should require personnel who refuse vaccination to complete a declination form." Because participation in Joint Commission accreditation is required for Medicare reimbursement, action taken by the Joint Commission to require interventions such as mandatory declination/consent forms might result in immediate action by health care organizations to follow these new standards and lead to higher vaccination rates among HCWs.^ 1“Frequently Asked Questions for H1N1 and Seasonal Influenza.” The Joint Commission - Infection Control: http://www.jointcommission.org/PatientSafety/InfectionControl/h1n1_faq.htm. ^

An evaluation of the centers for Medicare & Medicaid Services' Hospital Acquired Conditions and Present on Admission Indicator Reporting program

Objective: This dissertation evaluated three aspects of the Centers for Medicare and Medicaid Services' Hospital Acquired Conditions and Present on Admission Indicator Reporting program (HACPOA program) to produce three journal articles for publication. ^ Methods: All payer admission records from state inpatient databases from Arizona, New Jersey and Washington states were analyzed for the year 2008. However some analyses required a sample of adult only Medicare patients in the first two studies. California's inpatient data (2004 – 2010) was also analyzed in the third study to examine the reporting and non-payment program elements' impact on the incidence of hospital acquired conditions. ^ Results: Majority diagnoses reported in inpatient prospective payment systems hospitals were present on admission. However, some diagnoses are still coded as "not present on admission" and "insufficient documentation to determine whether or not conditions are present on admission or not". This is important because it reveals that hospital complications still occur in hospitals. Hospital fall and trauma injuries were the most common hospital acquired conditions observed in this study. Predictors of hospital fall injuries include age, gender, number of diagnoses, number of procedures, number of chronic conditions while predictors of hospital trauma injuries include number of e-codes, number of diagnoses and the presence of chronic conditions on a patient's admission records. Finally, the implementation of the present on admission reporting requirement increased reports of certain hospital acquired conditions while the non-payment policy element in the Hospital Acquired Conditions program reduced the incidence of hospital fall and trauma injuries in particular. ^ Conclusion: The implementation of the Hospital Acquired Conditions and Present on Admission Indicator Reporting program has made the state inpatient database a more useful source of data capable of now identifying hospital complications. The reporting and nonpayment program elements in the HACPOA program have also impacted the incidence of hospital acquired conditions. ^

ESPÍRITOS DO UNIVERSO RESPONSÁVEIS PELO DESTINO: ESTUDO EXEGÉTICO EM COLOSSENSES 2.8-3.4

Esta dissertação de mestrado analisará a expressão grega ta. stoicei/a tou/ ko,smou, “os elementos do mundo”, que ocorre na carta de Colossenses nos versículos 8 e 20 do segundo capítulo. Será feito um estudo exegético na perícope bíblica 2.8-3.4 da referida carta, bem como uma análise histórica especificamente do termo stoicei/a. O estudo desta expressão é importante para poder se compreender a filosofia colossense mencionada em Cl 2.8. A igreja cristã na cidade de Colossos estava inserida em um contexto social religioso sincrético. Esse sincretismo é percebido claramente em textos de magia como os Papiros Mágicos Gregos, muito comuns na região da Ásia Menor, a mesma onde a igreja colossense estava situada. O sincretismo religioso, envolvendo crenças judaicas e pagãs, reflete as bases dessa filosofia. O autor da carta aos Colossenses refuta a crença nos “elementos do mundo”, bem como a subserviência aos mesmos. Dentre outras crenças, acreditava-se que esses “elementos” poderiam influenciar os acontecimentos sobre a terra e o destino das pessoas. Questões que envolvem práticas acéticas, adoração a anjos e observância de calendário litúrgico, dão os contornos dessa filosofia. O autor da carta enfatiza o senhorio de Cristo, bem como as obras dele em favor dos cristãos colossenses, que proporcionavam a eles, segurança quanto a terem um bom destino. E, além disso, é assegurada uma liberdade aos cristãos colossenses que não podia lhes ser cerceada por quaisquer outras crenças religiosas. Então, as obras de Cristo, bem como o seu senhorio, são os principais argumentos utilizados pelo autor da carta, a fim de afirmar aos cristãos em Colossos que eles não precisam mais temer o destino e nem se submeter aos “elementos do mundo”.

Human Immunodeficiency Virus Reverse Transcriptase and Protease Sequence Database: an expanded data model integrating natural language text and sequence analysis programs

The HIV Reverse Transcriptase and Protease Sequence Database is an on-line relational database that catalogs evolutionary and drug-related sequence variation in the human immunodeficiency virus (HIV) reverse transcriptase (RT) and protease enzymes, the molecular targets of anti-HIV therapy (http://hivdb.stanford.edu). The database contains a compilation of nearly all published HIV RT and protease sequences, including submissions from International Collaboration databases and sequences published in journal articles. Sequences are linked to data about the source of the sequence sample and the antiretroviral drug treatment history of the individual from whom the isolate was obtained. During the past year 3500 sequences have been added and the data model has been expanded to include drug susceptibility data on sequenced isolates. Database content has also been integrated with didactic text and the output of two sequence analysis programs.

Mass extinctions and supernova explosions.

In a recent contribution to this journal Ellis and Schramm [Ellis, J. & Schramm, D. N. (1995) Proc. Natl. Acad. Sci. USA 92, 235-238] claim that supernova explosions can cause massive biological extinctions as a result of strongly enhanced stratospheric NOx (NO + NO2) production by accompanying galactic cosmic rays. They suggested that these NOx productions which would last over several centuries and occur once every few hundred million years would result in ozone depletions of about 95%, leading to vastly increased levels of biologically damaging solar ultraviolet radiation. Our detailed model calculations show, however, substantially smaller ozone depletions ranging from at most 60% at high latitudes to below 20% at the equator.