Interstellar neutral helium in the heliosphere from Interstellar Boundary Explorer observations. III. Mach number of the flow, velocity vector, and temperature from the first six years of measurements

We analyzed observations of interstellar neutral helium (ISN He) obtained from the Interstellar Boundary Explorer (IBEX) satellite during its first six years of operation. We used a refined version of the ISN He simulation model, presented in the companion paper by Sokol et al. (2015b), along with a sophisticated data correlation and uncertainty system and parameter fitting method, described in the companion paper by Swaczyna et al. We analyzed the entire data set together and the yearly subsets, and found the temperature and velocity vector of ISN He in front of the heliosphere. As seen in the previous studies, the allowable parameters are highly correlated and form a four-dimensional tube in the parameter space. The inflow longitudes obtained from the yearly data subsets show a spread of similar to 6 degrees, with the other parameters varying accordingly along the parameter tube, and the minimum chi(2) value is larger than expected. We found, however, that the Mach number of the ISN He flow shows very little scatter and is thus very tightly constrained. It is in excellent agreement with the original analysis of ISN He observations from IBEX and recent reanalyses of observations from Ulysses. We identify a possible inaccuracy in the Warm Breeze parameters as the likely cause of the scatter in the ISN He parameters obtained from the yearly subsets, and we suppose that another component may exist in the signal or a process that is not accounted for in the current physical model of ISN He in front of the heliosphere. From our analysis, the inflow velocity vector, temperature, and Mach number of the flow are equal to lambda(ISNHe) = 255 degrees.8 +/- 0 degrees.5, beta(ISNHe) = 5 degrees.16 +/- 0 degrees.10, T-ISNHe = 7440 +/- 260 K, nu(SNHe) = 25.8 +/- 0.4 km s(-1), and M-ISNHe = 5.079 +/- 0.028, with uncertainties strongly correlated along the parameter tube.

Driving and emergency braking may be impaired after tibiotalar joint arthrodesis: conclusions after a case series.

PURPOSE To assess whether reaction time (RT) and movement time (MT), as the two components of the total brake response time (TBRT) and brake force (BF) are different in patients with a foot joint arthrodesis in comparison to controls. METHODS The study was a comparative case series in a driving simulator under realistic driving conditions. Mobile patients without a walker, ≥6 months after surgery who were driving a car and had no neurological co-morbidity, knee or hip joint prosthesis were included in the study. The selection criteria resulted in 12 patients with right tibiotalar joint arthrodesis (TTJA) and 12 patients with another right foot joint arthrodesis (OFJA), who were compared to 17 individuals without any ankle-joint pathology. For TBRT, an empirical safe driving threshold of 700 ms was used. The outcome measures were RT, MT, TBRT, BF and McGuire score. RESULTS MT (p = 0.034) and TBRT (p = 0.026) were longer in TTJA patients in comparison with the controls. Also, more patients with TTJA than patients with OFJA and controls exceeded the safe driving threshold (p = 0.028). The outcomes in OFJA patients and in controls were comparable. The McGuire score was similar between the TTJA and OFJA patients (p = 0.26). CONCLUSIONS Significantly slower MT and TBRT, and significantly more patients exceeding the safe driving threshold, were observed after a tibiotalar-joint arthrodesis in comparison to the controls. Patients with OFJAs were not significantly different from the controls. Driving and emergency braking may be impaired after tibiotalar-joint arthrodesis.

Factors associated with diabetes in tuberculosis patients in Harris County, Texas 1995--2004

Objective. To determine the prevalence and factors associated with diabetes in tuberculosis patients in Harris County, Texas. ^ Background. Tuberculosis and diabetes mellitus are two diseases of immense public health significance. Various epidemiologic studies have established an association between the two conditions. While many studies have identified factors associated with the conditions individually, few have looked at factors associated with their co-occurrence particularly in the United States. Furthermore, most of those studies are hospital-based and may not be representative of the population. The aim of this study was to determine the prevalence and distribution of diabetes among tuberculosis patients in Harris County, Texas and to identify the factors associated with diabetes in tuberculosis. ^ Methods. A population-based case control study was performed using secondary data from the Houston Tuberculosis Initiative (HTI) collected from October 1995 to September 2004. Socio-demographic characteristics and clinical variables were compared between tuberculosis patients with diabetes and non-diabetic tuberculosis patients. Logistic regression analysis was performed to identify associations. Survival at 180 days post tuberculosis diagnosis was assessed by Cox regression. ^ Results. The prevalence of diabetes among the tuberculosis (TB) population was 14.4%. The diabetics (cases) with a mean age 53 ± 13.3 years were older than the non-diabetics (controls) with a mean age of 39 ± 18.5 years (p<0.001). Socio-demographic variables that were independently associated with the risk of diabetes were age (OR 1.04, p<0.001) and Hispanic ethnicity (OR 2.04, p<0.001). Diabetes was associated with an increased risk of pulmonary tuberculosis disease (OR 1.33, p<0.028). Among individuals with pulmonary TB, diabetes was associated with positive sputum acid-fast bacilli (AFB) smear (OR 1.47, p<0.005) and culture (OR 1.83, p<0.018). Diabetics were more likely to have cavitary lung disease than non-diabetics (OR 1.50, p<0.002). After adjustment for age and HIV status, the risk of dying within 180 days of TB diagnosis was significantly increased in the diabetics (HR 1.51, p<0.002). ^ Conclusion. Diabetes mellitus was more prevalent in our tuberculosis patients than in the general population. The tuberculous diabetic may be more infectious and has a higher risk of death. It is therefore imperative to screen diabetics for TB and TB patients for diabetes. ^

Analysis of prognostic factors for the development of metastases and survival in renal cell carcinoma patients

Introduction and objective. A number of prognostic factors have been reported for predicting survival in patients with renal cell carcinoma. Yet few studies have analyzed the effects of those factors at different stages of the disease process. In this study, different stages of disease progression starting from nephrectomy to metastasis, from metastasis to death, and from evaluation to death were evaluated. ^ Methods. In this retrospective follow-up study, records of 97 deceased renal cell carcinoma (RCC) patients were reviewed between September 2006 to October 2006. Patients with TNM Stage IV disease before nephrectomy or with cancer diagnoses other than RCC were excluded leaving 64 records for analysis. Patient TNM staging, Furhman Grade, age, tumor size, tumor volume, histology and patient gender were analyzed in relation to time to metastases. Time from nephrectomy to metastasis, TNM staging, Furhman Grade, age, tumor size, tumor volume, histology and patient gender were tested for significance in relation to time from metastases to death. Finally, analysis of laboratory values at time of evaluation, Eastern Cooperative Oncology Group performance status (ECOG), UCLA Integrated Staging System (UISS), time from nephrectomy to metastasis, TNM staging, Furhman Grade, age, tumor size, tumor volume, histology and patient gender were tested for significance in relation to time from evaluation to death. Linear regression and Cox Proportional Hazard (univariate and multivariate) was used for testing significance. Kaplan-Meier Log-Rank test was used to detect any significance between groups at various endpoints. ^ Results. Compared to negative lymph nodes at time of nephrectomy, a single positive lymph node had significantly shorter time to metastasis (p<0.0001). Compared to other histological types, clear cell histology had significant metastasis free survival (p=0.003). Clear cell histology compared to other types (p=0.0002 univariate, p=0.038 multivariate) and time to metastasis with log conversion (p=0.028) significantly affected time from metastasis to death. A greater than one year and greater than two year metastasis free interval, compared to patients that had metastasis before one and two years, had statistically significant survival benefit (p=0.004 and p=0.0318). Time from evaluation to death was affected by greater than one year metastasis free interval (p=0.0459), alcohol consumption (p=0.044), LDH (p=0.006), ECOG performance status (p<0.001), and hemoglobin level (p=0.0092). The UISS risk stratified the patient population in a statistically significant manner for survival (p=0.001). No other factors were found to be significant. ^ Conclusion. Clear cell histology is predictive for both time to metastasis and metastasis to death. Nodal status at time of nephrectomy may predict risk of metastasis. The time interval to metastasis significantly predicts time from metastasis to death and time from evaluation to death. ECOG performance status, and hemoglobin levels predicts survival outcome at evaluation. Finally, UISS appropriately stratifies risk in our population. ^

Comparison of compliance and immune response of drug users on the standard and accelerated hepatitis B vaccine schedules - Houston, Texas

Despite the availability of hepatitis B vaccine for over two decades, drug users and other high-risk adult populations have experienced low vaccine coverage. Poor compliance has limited efforts to reduce transmission of hepatitis B infection in this population. Evidence suggests that immunological response in drug users is impaired compared to the general population, both in terms of lower seroprotection rates and antibodies levels.^ The current study investigated the effectiveness of the multi-dose hepatitis B vaccine and compared the effect of the standard and accelerated vaccine schedules in a not-in-treatment, drug-using adult population in the city of Houston, USA.^ A population of drug-users from two communities in Houston, susceptible to hepatitis B, was sampled by outreach workers and referral methodology. Subjects were randomized either to the standard hepatitis vaccine schedule (0, 1-, 6-month) or to an accelerated schedule (0, 1-, 2-month). Antibody levels were detected through laboratory analyses at various time-points. The participants were followed for two years and seroconversion rates were calculated to determine immune response.^ A four percent difference in the overall compliance rate was observed between the standard (73%) and accelerated schedules (77%). Logistic regression analyses showed that drug users living on the streets were twice as likely to not complete all three vaccine doses (p=0.028), and current speedball use was also associated with non-completion (p=0.002). Completion of all three vaccinations in the multivariate analysis was also correlated with older age. Drug users on the accelerated schedule were 26% more likely to achieve completion, although this factor was marginally significant (p=0.085).^ Cumulative adequate protective response was gained by 65% of the HBV susceptible subgroup by 12-months and was identical for both the standard and accelerated schedules. Excess protective response (>=100 mIU/mL) occurred with greater frequency at the later period for the standard schedule (36% at 12-months compared to 14% at six months), while the greater proportion of excess protective response for the accelerated schedule occurred earlier (34% at 6 months compared to 18% at 12-months). Seroconversion at the adequate protective response level of 10 mIU/mL was reached by the accelerated schedule group at a quicker rate (62% vs. 49%), and with a higher mean titer (104.8 vs. 64.3 mIU/mL), when measured at six months. Multivariate analyses indicated a 63% increased risk of non-response for older age and confirmed the existence of an accelerating decline in immune response to vaccination manifesting after 40 years (p=0.001). Injecting more than daily was also highly associated with the risk of non-response (p=0.016).^ The substantial increase in the seroprotection rate at six months may be worth the trade-off against the faster antibody titer decrease and is recommended for enhancing compliance and seroconversion. Utilization of the accelerated schedule with the primary objective of increasing compliance and seroconversion rates during the six months after the first dose may confer early protective immunity and reduce the HBV vulnerability of drug users who continue, or have recently initiated, increased high risk drug use and sexual behaviors.^

An exploratory study of screening practices and barriers for postpartum depression in Texas

Purpose. To evaluate the prevalence of Postpartum Depression (PPD) screening among practicing obstetrician-gynecologists in Texas, and to identify factors and barriers associated with routine depression screening practices.^ Subjects. One hundred and eighty-nine fellows and junior fellows of the Texas Association of Obstetricians & Gynecologists (District XI).^ Methods. A survey questionnaire was developed and sent to 2,028 obstetriciangynecologists, asking about their current screening practices related to PPD. The survey questions were related to the physician's demographics, the patient population, screening practices, barriers to screening, and perceptions about resources in the community. Responses were analyzed to determine associations between these factors and the physician's screening practices. ^ Results. The respondents (n=189) constituted 9.3% of the surveyed population, thus the findings cannot be considered representative of all practicing Ob-Gyns in Texas. However, the following trends were observed. Of the respondents, 85.4% reported routinely screening for PPD, while 14.6% did not. However, of those that screened, only 20.2% used the Edinburgh Postnatal Depression Scale and 7.6% screened with the Postpartum Depression Screening Scale, both validated screening tools. The majority (77.2%) reported using an informal patient interview to screen. For those who did not routinely screen, inadequate training and inadequate resources to screen for PPD were the top two barriers. Physician's age was associated with routine screening practice, as older physicians were less likely to screen routinely. Primary insurance coverage of the patient population was also associated with screening practice; physicians with Medicaid and uninsured patients were less likely to screen routinely. Lastly, physicians that believed that adequate resources existed in their communities for the treatment of PPD were more likely to screen than those that did not.^ Conclusions. The present study is the first attempt at assessing Postpartum Depression screening practices and barriers in Texas. Although the response rate was low, the findings related to informal screening methods and inadequate training indicated that education and training with regards to PPD screening and validated screening tools among Ob-Gyns stand to be improved. Connecting physicians to psychiatric resources may also improve screening rates. This first look at screening practices in Texas serves as a platform for future research in order to gain definitive insight into the diagnosis and treatment of PPD, and ultimately design interventions to improve detection rates and treatment.^

Thrombolytic therapy for acute myocardial infarction: A cohort study to evaluate a selective approach to invasive diagnosis and therapy. The Corpus Christi Heart Project

Coronary perfusion with thrombolytic therapy and selective reperfusion by percutaneous transluminal coronary angioplasty (PTCA) were examined in the Corpus Christi Heart Project, a population-based surveillance program for hospitalized acute myocardial infarction (MI) patients in a biethnic community of Mexican-Americans (MAs) and non-Hispanic whites (NHWs). Results were based on 250 (12.4%) patients who received thromobolytic therapy in a cohort of 2011 acute MI cases. Out of these 107 (42.8%) underwent PTCA with a mean follow-up of 25 months. There were 186 (74.4%) men and 64 (25.6%) women; 148 (59.2%) were NHWs, 86 (34.4%) were MAs. Thrombolysis and PTCA were performed less frequently in women than in men, and less frequently in MAs than in NHWs.^ According to the coronary reperfusion interventions used, patients were divided in two groups, those that received no-PTCA (57.2%) and the other that underwent PTCA (42.8%) after thrombolysis. The case-fatality rate was higher in no-PTCA patients than in the PTCA (7.7% versus 5.6%), as was mortality at one year (16.2% versus 10.5%). Reperfusion was successful in 48.0% in the entire cohort and (51.4% versus 45.6%) in the PTCA and no-PTCA groups. Mortality in the successful reperfusion patients was 5.0% compared to 22.3% in the unsuccessful reperfusion group (p = 0.00016, 95% CI: 1.98-11.6).^ Cardiac catheterization was performed in 86.4% thrombolytic patients. Severe stenosis ($>$75%) obstruction was present most commonly in the left descending artery (52.8%) and in the right coronary artery (52.8%). The occurrence of adverse in-hospital clinical events was higher in the no-PTCA as compared to the PTCA and catheterized patients with the exception of reperfusion arrythmias (p = 0.140; Fisher's exact test p = 0.129).^ Cox regression analysis was used to study the relationship between selected variables and mortality. Apart from successful reperfusion, age group (p = 0.028, 95% CI: 2.1-12.42), site of acute MI index (p = 0.050) and ejection-fraction (p = 0.052) were predictors of long-term survival. The ejection-fraction in the PTCA group was higher than (median 78% versus 53%) in the no-PTCA group. Assessed by logistic regression analysis history of high cholesterol ($>$200mg/dl) and diabetes mellites did have significant prognostic value (p = 0.0233; p = 0.0318) in long-term survival irrespective of treatment status.^ In conclusion, the results of this study support the idea that the use of PTCA as a selective intervention following thrombolysis improves survival of patients with acute MI. The use of PTCA in this setting appears to be safe. However, we can not exclude the possibility that some of these results may have occurred due to the exclusion from PTCA of high risk patients (selection bias). ^

A case-control study to identify risk factors for preterm labor in Colorado Springs, Colorado

The study objectives were to determine risk factors for preterm labor (PTL) in Colorado Springs, CO, with emphasis on altitude and psychosocial factors, and to develop a model that identifies women at high risk for PTL. Three hundred and thirty patients with PTL were matched to 460 control patients without PTL using insurance category as an indirect measure of social class. Data were gathered by patient interview and review of medical records. Seven risk groups were compared: (1) Altitude change and travel; (2) Psychosocial ((a) child, sexual, spouse, alcohol and drug abuse; (b) neuroses and psychoses; (c) serious accidents and injuries; (d) broken home (maternal parental separation); (e) assault (physical and sexual); and (f) stress (emotional, domestic, occupational, financial and general)); (3) demographic; (4) maternal physical condition; (5) Prenatal care; (6) Behavioral risks; and (7) Medical factors. Analysis was by logistic regression. Results demonstrated altitude change before or after conception and travel during pregnancy to be non-significant, even after adjustment for potential confounding variables. Five significant psychosocial risk factors were determined: Maternal sex abuse (p = 0.006), physical assault (p = 0.025), nervous breakdown (p = 0.011), past occupational injury (p = 0.016), and occupational stress (p = 0.028). Considering all seven risk groups in the logistic regression, we chose a logistic model with 11 risk factors. Two risk factors were psychosocial (maternal spouse abuse and past occupational injury), 1 was pertinent to maternal physical condition ($\le$130 lbs. pre-pregnancy weight), 1 to prenatal care ($\le$10 prenatal care visits), 2 pertinent to behavioral risks ($>$15 cigarettes per day and $\le$30 lbs. weight gain) and 5 medical factors (abnormal genital culture, previous PTB, primiparity, vaginal bleeding and vaginal discharge). We conclude that altitude change is not a risk factor for PTL and that selected psychosocial factors are significant risk factors for PTL. ^

A descriptive analysis of the consumers at farm stands outside WIC clinics

Because fruit and vegetable intake remains low in low-income populations, the attention of public health researchers has focused on different strategies to reach this population. One possible method of reaching low income populations is through government food assistance programs like the WIC's Farmers Market Nutrition Program (FMNP). This program provides vouchers to WIC recipients that are redeemable only at farmers' markets. In the summer of 2010, two farm stands near WIC clinics in Austin were surveyed in order to establish socio-demographic characteristics of the clientele of the markets. The overall purpose of this pilot study was to describe the clientele of the markets and to examine associations between food insecurity, acculturation, socio-demographic factors, and farmers' market participants' fruit and vegetable intake. The sample was a convenience sample of farmers' market customers. One hundred study participants completed self-administered surveys. Independent t-tests were used to explore the differences in means of fruit and vegetable intake according to acculturation and food insecurity levels. The overall mean (SD) of daily fruit and vegetable intake was 4.20±2.69 for customers of both markets. Significant differences were reported between the two markets in overall fruit and vegetable intake and specifically in the following: 100% juice (P=.023), fruit consumption (P=.028), green salad (P=.003), and salsa (P=.044). The differences showed that customers at the market in a more busy location were on average reporting eating more fruits and vegetables than customers at another market that was located in a more secluded location. When examined by level of food security, individuals who were more food secure consumed more fruit (P=.016). When examined by level of acculturation, the overall fruit and vegetable intake was not significantly different between levels of acculturation. The overall findings in this report suggest that the population at these markets consists of individuals who are food insecure and on government assistance programs. While there were no significant differences between fruit and vegetable intake, acculturation and food insecurity, this report suggests the need for culturally tailored interventions that serve the Hispanic population and would assist this population to become more food secure.^

Differences in performance for quality of care indicators for acute myocardial infarction (AMI) across various hospital categories in Texas

The study analyzed Hospital Compare data for Medicare Fee-for-service patients at least 65 years of age to determine whether hospital performance for AMI outcome and processes of care measures differ amongst Texas hospitals with respect to ownership status (for profit vs. not-for-profit), academic status (teaching vs. non-teaching) and geographical setting (rural vs. urban). ^ The study found a statistically significant difference between for-profit and not-for-profit hospitals in four process-of-care measures (aspirin at discharge, P=0.028; ACE or ARB inhibitor for LSVD, P=0.048; Smoking cessation advice: P=0.034; outpatients who got aspirin with 24 hours of arrival in the ED, P=0.044). No significant difference in performance was found between COTH-member teaching and non-teaching hospitals for any of the eight process-of-care measures or the two outcome measures for AMI. The study was unable to compare performance based on geographic setting of hospitals due to lack of sufficient data for rural hospitals. ^ The results of the study suggest that for-profit Texas hospitals might be slightly better than not-for –profit hospitals at providing possible heart attack patients with certain processes of care.^

Incidence of enteric bacterial infections complicating Clostridium difficile infection (CDI)

The purpose of this study was to assess whether C. difficile infection (CDI) increases the risk of bacteremia or E. coli infection. The first specific aim of this study was to study the incidence of post C. difficile bacteremia in CDI patients stratified by disease severity vs. controls. The second specific aim was to study the incidence of post C. difficile E. coli infection from normally sterile sites stratified by disease severity vs. controls. This was a retrospective case case control study. The cases came from an ongoing prospective cohort study of CDI. Case group 1 were patients with mild to moderate CDI. Case group 2 were patients who had severe CDI. Controls were hospitalized patients given broad spectrum antibiotics that did not develop CDI. Controls were matched by age (±10 years) and duration of hospital visit (±1 week). 191 cases were selected from the cohort study and 191 controls were matched to the cases. Patients were followed up to 60 days after the initial diagnosis of CDI and assessed for bacteremia and E. coli infections. The Zar score was used to determine the severity of the CDI. Stata 11 was used to run all analyses. ^ The risk of non staphylococcal bacteremia after diagnosis of CDI was higher compared to controls (14% and 7% respectively, OR: 2.27; 95% CI:1.07-5.01, p=0.028). The risk of getting an E.coli infection was higher in cases than in controls (13% and 9% respectively although the results were not statistically significant (OR:1.4; 95% CI:0.38-5.59;p=0.32). Rates of non-staphylococcal bacteremia and E. coli infection did not differ cased on CDI severity. ^ This study showed that the risk of developing non-staphylococcus bacteremia was higher in patients with CDI compared to matched controls. The findings supported the hypothesis that CDI increases the risk of bacterial translocation specifically leading to the development of bacteremia.^

Prediction of sepsis in the burn intensive care unit patient

Sepsis is a significant cause for multiple organ failure and death in the burn patient, yet identification in this population is confounded by chronic hypermetabolism and impaired immune function. The purpose of this study was twofold: 1) determine the ability of the systemic inflammatory response syndrome (SIRS) and American Burn Association (ABA) criteria to predict sepsis in the burn patient; and 2) develop a model representing the best combination of clinical predictors associated with sepsis in the same population. A retrospective, case-controlled, within-patient comparison of burn patients admitted to a single intensive care unit (ICU) was conducted for the period January 2005 to September 2010. Blood culture results were paired with clinical condition: "positive-sick"; "negative-sick", and "screening-not sick". Data were collected for the 72 hours prior to each blood culture. The most significant predictors were evaluated using logistic regression, Generalized Estimating Equations (GEE) and ROC area under the curve (AUC) analyses to assess model predictive ability. Bootstrapping methods were employed to evaluate potential model over-fitting. Fifty-nine subjects were included, representing 177 culture periods. SIRS criteria were not found to be associated with culture type, with an average of 98% of subjects meeting criteria in the 3 days prior. ABA sepsis criteria were significantly different among culture type only on the day prior (p = 0.004). The variables identified for the model included: heart rate>130 beats/min, mean blood pressure<60 mmHg, base deficit<-6 mEq/L, temperature>36°C, use of vasoactive medications, and glucose>150 mg/d1. The model was significant in predicting "positive culture-sick" and sepsis state, with AUC of 0.775 (p < 0.001) and 0.714 (p < .001), respectively; comparatively, the ABA criteria AUC was 0.619 (p = 0.028) and 0.597 (p = .035), respectively. SIRS criteria are not appropriate for identifying sepsis in the burn population. The ABA criteria perform better, but only for the day prior to positive blood culture results. The time period useful to diagnose sepsis using clinical criteria may be limited to 24 hours. A combination of predictors is superior to individual variable trends, yet algorithms or computer support will be necessary for the clinician to find such models useful. ^

Modeling Techniques for the High-Resolution Interpretation of Cryo-Electron Microscopy Reconstructions

Essential biological processes are governed by organized, dynamic interactions between multiple biomolecular systems. Complexes are thus formed to enable the biological function and get dissembled as the process is completed. Examples of such processes include the translation of the messenger RNA into protein by the ribosome, the folding of proteins by chaperonins or the entry of viruses in host cells. Understanding these fundamental processes by characterizing the molecular mechanisms that enable then, would allow the (better) design of therapies and drugs. Such molecular mechanisms may be revealed trough the structural elucidation of the biomolecular assemblies at the core of these processes. Various experimental techniques may be applied to investigate the molecular architecture of biomolecular assemblies. High-resolution techniques, such as X-ray crystallography, may solve the atomic structure of the system, but are typically constrained to biomolecules of reduced flexibility and dimensions. In particular, X-ray crystallography requires the sample to form a three dimensional (3D) crystal lattice which is technically di‑cult, if not impossible, to obtain, especially for large, dynamic systems. Often these techniques solve the structure of the different constituent components within the assembly, but encounter difficulties when investigating the entire system. On the other hand, imaging techniques, such as cryo-electron microscopy (cryo-EM), are able to depict large systems in near-native environment, without requiring the formation of crystals. The structures solved by cryo-EM cover a wide range of resolutions, from very low level of detail where only the overall shape of the system is visible, to high-resolution that approach, but not yet reach, atomic level of detail. In this dissertation, several modeling methods are introduced to either integrate cryo-EM datasets with structural data from X-ray crystallography, or to directly interpret the cryo-EM reconstruction. Such computational techniques were developed with the goal of creating an atomic model for the cryo-EM data. The low-resolution reconstructions lack the level of detail to permit a direct atomic interpretation, i.e. one cannot reliably locate the atoms or amino-acid residues within the structure obtained by cryo-EM. Thereby one needs to consider additional information, for example, structural data from other sources such as X-ray crystallography, in order to enable such a high-resolution interpretation. Modeling techniques are thus developed to integrate the structural data from the different biophysical sources, examples including the work described in the manuscript I and II of this dissertation. At intermediate and high-resolution, cryo-EM reconstructions depict consistent 3D folds such as tubular features which in general correspond to alpha-helices. Such features can be annotated and later on used to build the atomic model of the system, see manuscript III as alternative. Three manuscripts are presented as part of the PhD dissertation, each introducing a computational technique that facilitates the interpretation of cryo-EM reconstructions. The first manuscript is an application paper that describes a heuristics to generate the atomic model for the protein envelope of the Rift Valley fever virus. The second manuscript introduces the evolutionary tabu search strategies to enable the integration of multiple component atomic structures with the cryo-EM map of their assembly. Finally, the third manuscript develops further the latter technique and apply it to annotate consistent 3D patterns in intermediate-resolution cryo-EM reconstructions. The first manuscript, titled An assembly model for Rift Valley fever virus, was submitted for publication in the Journal of Molecular Biology. The cryo-EM structure of the Rift Valley fever virus was previously solved at 27Å-resolution by Dr. Freiberg and collaborators. Such reconstruction shows the overall shape of the virus envelope, yet the reduced level of detail prevents the direct atomic interpretation. High-resolution structures are not yet available for the entire virus nor for the two different component glycoproteins that form its envelope. However, homology models may be generated for these glycoproteins based on similar structures that are available at atomic resolutions. The manuscript presents the steps required to identify an atomic model of the entire virus envelope, based on the low-resolution cryo-EM map of the envelope and the homology models of the two glycoproteins. Starting with the results of the exhaustive search to place the two glycoproteins, the model is built iterative by running multiple multi-body refinements to hierarchically generate models for the different regions of the envelope. The generated atomic model is supported by prior knowledge regarding virus biology and contains valuable information about the molecular architecture of the system. It provides the basis for further investigations seeking to reveal different processes in which the virus is involved such as assembly or fusion. The second manuscript was recently published in the of Journal of Structural Biology (doi:10.1016/j.jsb.2009.12.028) under the title Evolutionary tabu search strategies for the simultaneous registration of multiple atomic structures in cryo-EM reconstructions. This manuscript introduces the evolutionary tabu search strategies applied to enable a multi-body registration. This technique is a hybrid approach that combines a genetic algorithm with a tabu search strategy to promote the proper exploration of the high-dimensional search space. Similar to the Rift Valley fever virus, it is common that the structure of a large multi-component assembly is available at low-resolution from cryo-EM, while high-resolution structures are solved for the different components but lack for the entire system. Evolutionary tabu search strategies enable the building of an atomic model for the entire system by considering simultaneously the different components. Such registration indirectly introduces spatial constrains as all components need to be placed within the assembly, enabling the proper docked in the low-resolution map of the entire assembly. Along with the method description, the manuscript covers the validation, presenting the benefit of the technique in both synthetic and experimental test cases. Such approach successfully docked multiple components up to resolutions of 40Å. The third manuscript is entitled Evolutionary Bidirectional Expansion for the Annotation of Alpha Helices in Electron Cryo-Microscopy Reconstructions and was submitted for publication in the Journal of Structural Biology. The modeling approach described in this manuscript applies the evolutionary tabu search strategies in combination with the bidirectional expansion to annotate secondary structure elements in intermediate resolution cryo-EM reconstructions. In particular, secondary structure elements such as alpha helices show consistent patterns in cryo-EM data, and are visible as rod-like patterns of high density. The evolutionary tabu search strategy is applied to identify the placement of the different alpha helices, while the bidirectional expansion characterizes their length and curvature. The manuscript presents the validation of the approach at resolutions ranging between 6 and 14Å, a level of detail where alpha helices are visible. Up to resolution of 12 Å, the method measures sensitivities between 70-100% as estimated in experimental test cases, i.e. 70-100% of the alpha-helices were correctly predicted in an automatic manner in the experimental data. The three manuscripts presented in this PhD dissertation cover different computation methods for the integration and interpretation of cryo-EM reconstructions. The methods were developed in the molecular modeling software Sculptor (http://sculptor.biomachina.org) and are available for the scientific community interested in the multi-resolution modeling of cryo-EM data. The work spans a wide range of resolution covering multi-body refinement and registration at low-resolution along with annotation of consistent patterns at high-resolution. Such methods are essential for the modeling of cryo-EM data, and may be applied in other fields where similar spatial problems are encountered, such as medical imaging.