Re-examining the spectra of macromolecules. Current practice of spectral quasi B-factor flattening.

The analysis of structure factors in 3D cryo-EM Coulomb potential maps and their "enhancement" at the end of the reconstruction process is a well-established practice, normally referred to as sharpening. The aim is to increase contrast and, in this way, to help tracing the atomic model. The most common way to accomplish this enhancement is by means of the so-called B-factor correction, which applies a global filter to boost high frequencies with some dampening considerations related to noise amplification. The results are maps with a better visual aspect and a quasiflat spectrum at medium and high frequencies. This practice is so widespread that most map depositions in the Electron Microscopy Data Base (EMDB) only contain sharpened maps. Here, the use in cryoEM of global B-factor corrections is theoretically and experimentally analyzed. Results clearly illustrate that protein spectra present a falloff. Thus, spectral quasi-flattening may produce protein spectra with distortions when compared with experimental ones, this fact, combined with the practice of reporting only sharpened maps, generates a sub-optimal situation in terms of data preservation, reuse and reproducibility. Now that the field is more advanced, we put forward two suggestions: (1) to use methods which keep more faithfully the original experimental signal properties of macromolecules when "enhancing" the map, and (2) to further stress the need to deposit the original experimental maps without any postprocessing or sharpening, not only the enhanced maps. In the absence of access to these original maps data is lost, preventing their future analysis with new methods.

Temporal trends in chronic obstructive pulmonary disease mortality in Mexico, 1999-2014.

SETTING: Country of Mexico. OBJECTIVE: To determine mortality trends due to chronic obstructive pulmonary disease (COPD) in Mexico between 1999 and 2014. DESIGN: COPD mortality data for persons aged ≥40 years from 1999 to 2014 were obtained from the official website of the Mexican Ministry of Health. Age-standardised mortality rates (ASMRs) were calculated, and joinpoint regression analysis was used to identify trends over time. The annual per cent change (APC) was determined for each trend. RESULTS: A total of 313,962 COPD deaths (crude rate 66.3 per 100,000 population) was reported. Between 1999 and 2014, overall ASMRs decreased from 75.5 to 62.2/100,000 (APC -0.6, P = 0.03): from 94 to 74.7 (APC -0.8, P = 0.004) in males and from 59.7 to 51.8 (APC -0.2, P = 0.4) in females. CONCLUSIONS: COPD mortality rates in Mexico are slowly declining overall and among males. The reduction in smoking prevalence over time, and the new cigarette taxes and smoking laws implemented during the study period, have had no immediate impact on mortality. The lack of a decline in COPD mortality among females needs to be further investigated, particularly in rural areas, where the prevalence of biomass smoke exposure remains high.

Frequency analysis for an extended photoacoustic transport model.

In photoacoustic imaging, the signal attenuation is a well-known source of artifacts over the image reconstruction. It is recognized that this is caused by optical absorption effects and by the ultrasound broadband scattering. However, the sound dispersion is generally neglected, although it appears notably in thick or heterogeneous tissues. In the present Letter, we give an experimental example in which both attenuation and sound dispersion are dealt with as relevant features to be taken into consideration. An analytic perspective of these perturbations leads us to a waveform transport-model extension that provides a linear description of the induced acoustic effects. We find a near match between the theoretical predictions and the experimental results in the frequency domain. These outcomes approximate projection data that represent forward solutions in photoacoustic image reconstruction.

No one likes a copycat: a cross-cultural investigation of children's response to plagiarism.

Copying other people's ideas is evaluated negatively by American children and adults. The current study investigated the influence of culture on children's evaluations of plagiarism by comparing children from three countries--the United States, Mexico, and China--that differ in terms of their emphasis on the protection of intellectual property and ideas. Children (3- to 6-year-olds) were presented with videos involving two characters drawing pictures and were asked to evaluate the character who drew unique work or the character who copied someone else's drawing. The study showed that 5- and 6-year-olds from all three cultures evaluated copiers negatively compared with unique drawers. These results suggest that children from cultures that place different values on the protection of ideas nevertheless develop similar concerns with plagiarism by 5-year-olds.

Reconstruction from a Few Projections by ℓ(1)-Minimization of the Haar Transform.

Much recent activity is aimed at reconstructing images from a few projections. Images in any application area are not random samples of all possible images, but have some common attributes. If these attributes are reflected in the smallness of an objective function, then the aim of satisfying the projections can be complemented with the aim of having a small objective value. One widely investigated objective function is total variation (TV), it leads to quite good reconstructions from a few mathematically ideal projections. However, when applied to measured projections that only approximate the mathematical ideal, TV-based reconstructions from a few projections may fail to recover important features in the original images. It has been suggested that this may be due to TV not being the appropriate objective function and that one should use the ℓ(1)-norm of the Haar transform instead. The investigation reported in this paper contradicts this. In experiments simulating computerized tomography (CT) data collection of the head, reconstructions whose Haar transform has a small ℓ(1)-norm are not more efficacious than reconstructions that have a small TV value. The search for an objective function that provides diagnostically efficacious reconstructions from a few CT projections remains open.

[Joint position statement of the Mexican College of Orthopedics and Traumatology: prophylaxis for venous thromboembolic disease in high-risk orthopedic surgery]. / Declaración de posición conjunta del Colegio Mexicano de Ortopedia y Traumatología: profilaxis de la enfermedad tromboembólica venosa en cirugía ortopédica de alto riesgo.

Venous thromboembolic disease (VTED) is a public health problem worldwide. In the United States it causes 2 million annual cases. Its annual incidence is 1-2 cases per 1,000 individuals in the general population. It is a disease frequently associated with life threatening complications and its mortality rate is 1-5% of cases. Due to its high complication rate, its slow recovery, and the need for prolonged disability, it is considered as a high-cost disease. VTED may occur in both surgical and medical patients; the known associated risk factors include prolonged rest, active cancer, congestive heart failure, atrial fibrillation, and stroke, among the major medical conditions. Orthopedic surgery represents the main surgical risk factor for VTED, including mainly hip and knee replacements, as well as polytraumatized patients with severe spinal lesions, and major fractures. VTED may be prevented with the appropriate use of antithrombotics. The participants in this consensus defined thromboprophylaxis as the strategy and actions undertaken to reduce the risk of VTED in patients undergoing high risk orthopedic surgery. The position of the Mexican College of Orthopedics and Traumatology regarding the prevention of VTED in orthopedic surgery is described herein.

[Activity of daptomycin, ciprofloxacin, clindamycin and cotrimoxazole against coagulase-negative Staphylococcus strains with diminished susceptibility to vancomycin]. / Actividad de daptomicina, ciprofloxacino, clindamicina y cotrimoxazol frente a diferentes cepas de Staphylococcus coagulasa negativo con sensibilidad conservada y disminuida para vancomicina.

INTRODUCTION: Coagulase Negative Staphylococci (CNS) have become one of the most common nosocomial pathogens and it has a high mortality rate due to the increased of seriously ill patients survival, long states immunosuppression and presence of foreign bodies, such as catheters, prostheses, pacemakers, etc. In addition, there is a significant increase in resistance to antimicrobial drugs, especially beta-lactams, and the increase in the MIC for vancomycin leads to a loss of clinical efficacy. This necessitates the search for new therapeutic alternatives, such as daptomycin. The aim of this paper is to study the activity of daptomycin, ciprofloxacin, clindamycin and cotrimoxazole in two groups of clinically significant CNS: a MIC90with vancomycin ≤ 1 mg/L and the other with MIC90 2 mg/L. METHODS: We identified and studied MIC90 to ciprofloxacin, clindamycin and cotrimoxazole from 54 strains of clinically significant by the CNS Combo 22 Microscan panels (Dade Behring, Siemens). The MIC90for daptomycin was performed using Etest (AB BioMérieux, Solna, Sweden) on Mueller Hinton plates (BioMérieux, France). RESULTS: In Group I (vancomycin MIC90 ≤ 1 mg/L) were 19 strains whereas in Group II (vancomycin MIC90 =2 mg/L) were 35 strains. Expressed in mg/L, MIC90 ranges for daptomycin were 0.047-0.5 in Group I and 0.064-0.5 in Group II. for ciprofloxacin were 8 sensitive strains and 11 resistant in Group I and 10 sensitive and 25 resistant in Group II. For clindamycin were 7 sensitive strains and 12 resistant in Group I and 16 sensitive and 19 resistant in Group II. Finally, for cotrimoxazole were 10 sensitive strains and 9 resistant in Group I and 19 sensitive and 16 resistant in Group II. CONCLUSIONS: The MIC levels to daptomycin were not influenced by the increase in the MIC for vancomycin. There was no statistically significant difference for the sensitivity of ciprofloxacin between the two groups of vancomycin. Regardless of vancomycin, there were a clear relationship between the sensitivity of ciprofloxacin with clindamycin and cotrimoxazole.

Demographic risk factors of pulmonary colonization by non-tuberculous mycobacteria.

SETTING: British Columbia (BC), Canada. OBJECTIVE: To determine the risk factors for pulmonary colonization by non-tuberculous mycobacteria (NTM). DESIGN: Retrospective study of subjects colonized by NTM from 1990 to 2006. Subjects without mycobacterial disease and with at least three negative cultures served as controls. RESULTS: Mycobacterium avium complex (MAC) species were the most common NTM. Risk factors of colonization included age > or = 60 years (aOR 2.3), female sex (aOR 1.2), residency in Canada for at least 10 years (aOR 3.8), Canadian-born aboriginal (aOR 1.8), and Canadian-born non-aboriginal (aOR 1.4). Predictors of MAC colonization included White race (aOR 1.6) and residency in Canada for at least 10 years, which was the strongest predictor (aOR 6.7). Aboriginal origin was associated with non-MAC colonization (aOR 1.8), and Canadian-born people from the East/South-East Asian ethnic groups were protected from MAC colonization (aOR 0.2), all aOR P < 0.05. CONCLUSION: Older age, female sex, having been born in Canada, long residency in BC and White race predict pulmonary NTM colonization, while Aboriginal origin predicts non-MAC colonization. Further research is needed to identify environmental NTM sources in BC and to determine their relation to colonization and disease.

The incidence of pulmonary non-tuberculous mycobacteria in British Columbia, Canada.

SETTING: British Columbia Centre for Disease Control (BCCDC), Vancouver, Canada. OBJECTIVE: To determine the incidence of non-tuberculous mycobacteria (NTM) and to assess the impact of new laboratory techniques. DESIGN: Population-based study of all subjects with positive cultures for NTM from 1990 to 2006. RESULTS: Mycobacterium avium complex (MAC) was the most common NTM isolate (77%). The median incidence rates per 100 000 population in the total sample were respectively 6.7, 4.5 and <0.7 for all NTMs, MAC and all non-MAC species; for NTM-treated subjects the rates were respectively 1.6, 1.4 and <0.08; and for the NTM-colonised they were respectively 4.7, 2.7 and <0.5. In the period after the introduction of new laboratory techniques, all NTM isolates, the overall MAC rate and the MAC-colonised rate increased by respectively 24%, 35.4% and 76% (P < 0.05). All NTM isolates and rates for all NTMs, NTM-treated and M. tuberculosis subjects (used as comparison group) decreased over time (P < 0.05). CONCLUSION: The most common NTM species was MAC. Episodic increases in the number of isolates and incidence rates of subjects colonised with MAC are likely to be associated with the implementation of new laboratory techniques, which may represent an artefact. The decrease in rates of NTM-treated subjects is reassuring.

Influence of testing methodology on the tigecycline activity profile against presumably tigecycline-non-susceptible Acinetobacter spp.

OBJECTIVES: To compare the tigecycline activity profile against Acinetobacter spp. by Etest versus broth microdilution in isolates with high Etest MIC. METHODS: Acinetobacter spp. isolates with tigecycline MICs of >or=0.5 mg/L determined by commercially developed Etests strips (January 2006 to July 2007) in five Spanish hospitals were considered. Values were rounded to the nearest upper double-dilution. Susceptibility by broth microdilution following CLSI (formerly NCCLS) recommendations, as the reference method, was determined in a central laboratory. BSAC breakpoints were used: susceptible 2 mg/L. RESULTS: One hundred and forty-eight isolates were collected: 12 isolates with a tigecycline Etest MIC of 0.5 mg/L, 14 with 1 mg/L, 86 with 2 mg/L, 31 with 4 mg/L and 5 with 8 mg/L. Isolates with Etest MICs of 0.5-1 mg/L showed the same values by broth microdilution. Among isolates with Etest MICs of 2 mg/L, only 5.8% of strains showed the same value by both methods (88.4% showed values that were one or two dilutions lower by microdilution). None of the 36 isolates with Etest MICs of 4-8 mg/L showed the same value by both methods, with values at least two dilutions lower by microdilution. Weak correlation (R = 0.238; P or=2 mg/L for Acinetobacter spp. since strains with Etest MICs of 2-4 mg/L are susceptible when tested by microdilution. False non-susceptibility by Etest may exclude tigecycline as a therapeutic option in a field where multiresistance is the rule.

Risk of tuberculosis in screened subjects without known risk factors for active disease.

SETTING: Tuberculosis (TB) referral clinic in Vancouver, British Columbia, Canada. BACKGROUND: Screening for and treatment of latent TB infection (LTBI) in at-risk populations are the cornerstone of TB control in low-incidence countries. Persons at low risk often undergo the tuberculin skin test (TST) for reasons other than contact. Little information exists on the actual risk of TB in this population. OBJECTIVE: To determine the risk of TB in screened subjects without known risk factors. DESIGN: Retrospective descriptive analysis of demographics, TST reaction size and TB disease occurrence in 98333 low-risk subjects screened from 1990 to 2002. RESULTS: The average annual disease rate was 0.4 per 100000 population (cumulative rate 7.4/100000) from 1990 to 2006, and TB was diagnosed only in the foreign-born. Risk of TB in the foreign-born increased with larger TST reaction size (P < 0.03). Completion of treatment for LTBI was not documented for any of the subsequent active TB cases. CONCLUSION: In a low-risk screened population, active TB disease was found only in the foreign-born. Treatment of LTBI is not recommended in persons with a positive TST and no additional risk factors. Local screening programs should focus on populations with confirmed risk factors for disease.

The prevalence and predictors of tuberculin positivity in subjects screened for reasons other than contact investigation.

BACKGROUND: No previous studies have estimated the rates of tuberculin positivity (TP) in noncontact populations within the same community, which is important for prioritizing and implementing preventive measures. OBJECTIVES: To estimate the prevalence and predictors of TP in noncontact populations. METHODS: A retrospective analysis of tuberculin results of noncontact populations screened in British Columbia from 1990 to 2002 was conducted. RESULTS: The period prevalence of TP in 59,791 screened subjects was 12.7% (95% CI 12.4% to 13.0%), 30.4% (95% CI 28.2% to 32.7%) and 60.9% (95% CI 60.3% to 61.6%) for Canadian-born non-Aboriginals (CBNAs), Canadian-born Aboriginals (CBAs) and foreign born (FB), respectively. After controlling for age and sex, independent predictors of TP included Bacille Calmette-Guérin (BCG) vaccination (OR 19.6, 95% CI 17.9 to 21.5), country of birth (CBA: OR 2.87, 95% CI 2.44 to 3.37; FB: OR 3.67, 95% CI 3.34 to 4.03) and the following populations: correctional centre residents (OR 4.14, 95% CI 1.87 to 9.15), residents of long-term care and community care facilities (OR 1.79, 95% CI 1.44 to 2.23), immigrants (OR 1.75, 95 % CI 1.50 to 2.04), health centre employees (OR 1.71, 95 % CI 1.56 to 1.88), volunteers (OR 1.38, 95% CI 1.14 to 1.68), self-referred healthy subjects (OR 1.30, 95% CI 1.15 to 1.48) and students (OR 1.27, 95% CI 1.19 to 1.35). CBAs, FB and male subjects were less likely to react to tuberculin than CBNAs and female subjects among those vaccinated with Bacille Calmette-Guérin (P<0.05). CONCLUSIONS: Rates of TP correlate with disease rates by sex and origin. The continuation of tuberculin screening programs is warranted in noncontact populations with high TP rates, where unknown exposure to active cases is more likely to occur. Further research is needed to determine the reasons why a higher response to tuberculin occurs in BCG-vaccinated women and CBNAs.

Exposure to therapeutic concentrations of ritonavir, but not saquinavir, reduces secreted aspartyl proteinase of Candida parapsilosis.

The effect of ritonavir and saquinavir, HIV proteinase inhibitors, on the secreted aspartyl proteinase (Sap) activity of Candida parapsilosis was studied. In a proteinase-inducing medium (yeast carbon base-bovine serum albumin), Sap activity in all clinical isolates of C. parapsilosis (n = 20) was observed at 37 degrees C but not at 22 degrees C. The presence of ritonavir at a concentration of 8 microg/ml produced an inhibition close to 50% albumin consumption and also delayed yeast growth; however, saquinavir did not have any effect on growth or on Sap activity. In Sabouraud broth, which does not induce Sap production, no effect was shown on yeast growth by either of the two HIV proteinase inhibitors studied.

Risk of tuberculosis in children from smear-negative source cases.

SETTING: British Columbia, Canada. OBJECTIVE: To determine the frequency of smear-negative tuberculosis (TB) transmission events from adults to children in epidemiologically linked pairs and to determine the predictors for identifying the source case. DESIGN: We extracted demographic, clinical and mycobacteriology information of 190 children with TB and their 83 source cases reported from 1990 to 2001 in the province of British Columbia. Smear-negative transmission events from adults to children were determined by identifying the smear results of epidemiologically linked source cases. We compared the sex, age, ethnicity, contact history, site of disease and tuberculin skin test (TST) results of children who had a source case identified with those who had not. RESULTS: Smear-negative source cases transmitted the disease to 10% of children (95%CI 5-17). Aboriginals (OR 4.9, 95%CI 1.5-13.4), those with primary TB (OR 7.3, 95%CI 3.3-16.0) and those with a positive TST (OR 2.9, 95%CI 1.2-7.0) were independent predictors for source case identification. CONCLUSION: This study suggests lower rates of transmission of disease to children from smear-negative sources compared to other studies involving all ages. Ethnicity of children, site of disease and a positive TST predict source case identification.

Wood smoke exposure and lung adenocarcinoma in non-smoking Mexican women.

OBJECTIVE: To determine the association between long-term exposure to wood smoke from cooking and lung adenocarcinoma in non-smoking Mexican women. METHODS: We reviewed records of hospitalized patients at a chest referral hospital in Mexico City and identified 113 histologically proven lung adenocarcinoma cases in non-smoking women. Four control groups of non-smoking women were also selected: 99 patients with pulmonary tuberculosis (PTB), 110 with interstitial lung disease (ILD), 64 with miscellaneous pulmonary conditions (MISC), and the three control groups combined (COMB) (n = 273). RESULTS: Exposure was assessed on the basis of questionnaire responses at the time of hospital admission. Exposure to wood smoke for more than 50 years, but not for shorter periods, was associated with lung cancer after adjusting for age, education, socio-economic status and environmental tobacco smoke (ETS) exposure. Adjusted odds ratios from the multivariable logistic regression models were 1.4 (95%CI 0.6-2.0) for cases vs. TB controls, 1.9 (95%CI 0.9-4.0) for cases vs. ILD controls, 2.6 (95%CI 1.0-6.3) for cases vs. MISC controls and 1.9 (95%CI 1.1-3.5) for cases vs. COMB controls. CONCLUSION: These findings suggest that long-term exposure to wood smoke from cooking may contribute to the development of lung cancer.

Transmission of tuberculosis from smear negative patients: a molecular epidemiology study.

BACKGROUND: While smear positive patients with tuberculosis (TB) are considered more infectious than smear negative patients, the latter can also transmit TB. METHODS: In a molecular epidemiology study of 791 patients in the Greater Vancouver regional district, the number of episodes of TB transmission from two groups of smear negative clustered patients by RFLP (assumed to be involved in recent transmission) was estimated after assessing for potential bias. Group 1 (n = 79) included patients with pulmonary TB or pulmonary + extrapulmonary disease (PTB or PTB+EPTB); group 2 (n = 129) included all patients in group 1 + extrapulmonary cases alone. RESULTS: In the total sample the mean (SD) age was 51 (21) years, 54.3% were male, and 17.0% of patients were clustered. Compared with smear negative patients, smear positive patients were more likely to be in a cluster (OR = 2.0, 95% CI 1.1 to 3.6) and to have had a history of ethanol abuse (OR = 2.7, 95% CI 1.0 to 6.7), diabetes mellitus (OR = 2.8, 95% CI 1.1 to 7.0), injection drug use (OR = 3.1, 95% CI 1.1 to 8.3), and to have had a previous hospital admission (OR = 8.5, 95% CI 5.1 to 14.0). The proportion of episodes of transmission from smear negative clustered patients ranged from 17.3% to 22.2% in group 1 and from 25% to 41% in group 2. CONCLUSION: In Greater Vancouver, smear negative cases appear responsible for at least one sixth of culture positive episodes of TB transmission.

The content of glycogen phosphorylase and glycogen in preparations of sarcoplasmic reticulum-glycogenolytic complex is enhanced in diabetic rat skeletal muscle.

AIMS/HYPOTHESIS: We have examined the effect of diabetes and pharmacological insulin treatment on the content of glycogen phosphorylase and glycogen associated with the sarcoplasmic reticulum-glycogenolytic complex from rat skeletal muscle. METHODS: Diabetes was induced in rats by streptozotocin injection. Enzymatic activities were measured using spectrophotometric methods. Glycogen phosphorylase was determined measuring the pyridoxal-5' -phosphate content and using polyacrylamide gel electrophoresis. Glycogen content was measured by enzymatic and the phenol sulfuric methods. RESULTS: The content of glycogen phosphorylase associated with the sarcoplasmic reticulum glycogenolytic complex gradually arises after diabetes induction. The content of glycogen phosphorylase was restored to a control value by pharmacological insulin treatment. In addition, the content of glycogen in preparations of sarcoplasmic reticulum-glycogenolytic complex of diabetic animals was also increased, whereas the content of glycogen in total muscle of diabetic rats was similar to that of the control rats. The absolute and relative amount of glycogen associated with sarcoplasmic reticulum seemed to increase in diabetic animals. These effects on the compartmentalisation of glycogen were suppressed by insulin treatment. Additionally, the rate of conversion of glycogen phosphorylase b to a, an index of the phosphorylase kinase activity, was 50 % lower in diabetic rats, increasing the dephosphorylated form of glycogen phosphorylase and, as a consequence, its association with sarcoplasmic reticulum membranes. CONCLUSION/INTERPRETATION: These results suggest that under diabetic conditions, both glycogen phosphorylase and a small percentage of muscle glycogen are relocalized in the sarcoplasmic reticulum-glycogenolytic complex.