Where do we aspire to publish? A position paper on scientific communication in biochemistry and molecular biology.

The scientific publication landscape is changing quickly, with an enormous increase in options and models. Articles can be published in a complex variety of journals that differ in their presentation format (online-only or in-print), editorial organizations that maintain them (commercial and/or society-based), editorial handling (academic or professional editors), editorial board composition (academic or professional), payment options to cover editorial costs (open access or pay-to-read), indexation, visibility, branding, and other aspects. Additionally, online submissions of non-revised versions of manuscripts prior to seeking publication in a peer-reviewed journal (a practice known as pre-printing) are a growing trend in biological sciences. In this changing landscape, researchers in biochemistry and molecular biology must re-think their priorities in terms of scientific output dissemination. The evaluation processes and institutional funding for scientific publications should also be revised accordingly. This article presents the results of discussions within the Department of Biochemistry, University of São Paulo, on this subject.

Where do we aspire to publish? A position paper on scientific communication in biochemistry and molecular biology

The scientific publication landscape is changing quickly, with an enormous increase in options and models. Articles can be published in a complex variety of journals that differ in their presentation format (online-only or in-print), editorial organizations that maintain them (commercial and/or society-based), editorial handling (academic or professional editors), editorial board composition (academic or professional), payment options to cover editorial costs (open access or pay-to-read), indexation, visibility, branding, and other aspects. Additionally, online submissions of non-revised versions of manuscripts prior to seeking publication in a peer-reviewed journal (a practice known as pre-printing) are a growing trend in biological sciences. In this changing landscape, researchers in biochemistry and molecular biology must re-think their priorities in terms of scientific output dissemination. The evaluation processes and institutional funding for scientific publications should also be revised accordingly. This article presents the results of discussions within the Department of Biochemistry, University of São Paulo, on this subject.

Computed Tomography Findings of Bronchiectasis in Different Respiratory Phases Correlate with Pulmonary Function Test Data in Adults.

OBJECTIVE: To investigate bronchiectasis variations in different computed tomography (CT) respiratory phases, and their correlation with pulmonary function test (PFT) data, in adults. METHODS: Retrospective data analysis from 63 patients with bronchiectasis according to CT criteria selected from the institution database and for whom PFT data were also available. Bronchiectasis diameter was measured on inspiratory and expiratory phases. Its area and matched airway-vessel ratios in both phases were also calculated. Finally, PFT results were compared with radiological measurements. RESULTS: Bronchiectatic airways were larger on inspiration than on expiration (mean cross-sectional area, 69.44 vs. 40.84 mm2; p < 0.05) as were airway-vessel ratios (2.1 vs. 1.4; p < 0.05). Cystic bronchiectasis cases showed the least variation in cross-sectional area (48%). Mean predicted values of forced expiratory volume in 1 s (FEV1) and forced vital capacity (FVC) were 81.5 and 77.2%, respectively, in the group in which bronchiectasis could not be identified on expiratory images, and 58.3 and 56.0%, respectively, in the other group (p < 0.05). Variation in bronchiectasis area was associated with poorer lung function (r = 0.32). CONCLUSION: Bronchiectasis detection, diameter, and area varied significantly according to CT respiratory phase, with non-reducible bronchiectasis showing greater lung function impairment.

Optimization of the Production of Inactivated Clostridium novyi Type B Vaccine Using Computational Intelligence Techniques.

Clostridium novyi causes necrotic hepatitis in sheep and cattle, as well as gas gangrene. The microorganism is strictly anaerobic, fastidious, and difficult to cultivate in industrial scale. C. novyi type B produces alpha and beta toxins, with the alpha toxin being linked to the presence of specific bacteriophages. The main strategy to combat diseases caused by C. novyi is vaccination, employing vaccines produced with toxoids or with toxoids and bacterins. In order to identify culture medium components and concentrations that maximized cell density and alpha toxin production, a neuro-fuzzy algorithm was applied to predict the yields of the fermentation process for production of C. novyi type B, within a global search procedure using the simulated annealing technique. Maximizing cell density and toxin production is a multi-objective optimization problem and could be treated by a Pareto approach. Nevertheless, the approach chosen here was a step-by-step one. The optimum values obtained with this approach were validated in laboratory scale, and the results were used to reload the data matrix for re-parameterization of the neuro-fuzzy model, which was implemented for a final optimization step with regards to the alpha toxin productivity. With this methodology, a threefold increase of alpha toxin could be achieved.

Addition of metal ions to a (hemi)cellulolytic enzymatic cocktail produced in-house improves its activity, thermostability, and efficiency in the saccharification of pretreated sugarcane bagasse.

High activity and stability are essential for (hemi)cellulolytic enzymes used in biomass conversion, while non-productive binding of cellulases to lignin reduces saccharification efficiency and needs to be avoided. One potential strategy is the addition of inexpensive metal ions. This paper describes the influence of divalent metal ions on the activity, thermostability, and saccharification efficiency of (hemi)cellulolytic enzymes produced in-house by Aspergillus niger under solid-state fermentation (SSF). The use of Mn(2+) provided the best (hemi)cellulolytic activity and stability, with an increase in endoglucanase activity of up to 57%. The use of Mn(2+) was then investigated in the saccharification of sugarcane bagasse submitted to acid, steam-explosion, and hydrothermal pretreatments. The addition of Mn(2+) ions at 10mM in the saccharification of acid-pretreated bagasse resulted in a 34% increase in glucose release. These positive effects appeared to be due to a reduction in non-productive enzyme adsorption. The findings suggest that the addition of inexpensive metal ions can help to improve activity, thermostability, and saccharification efficiency of (hemi)cellulolytic enzymes.

Computed tomographic pulmonary changes in patients with chronic rhinosinusitis.

OBJECTIVE: To investigate whether patients with a diagnosis of chronic rhinosinusitis (CRS) show characteristic pulmonary changes on chest CT compared with a control group without sinusopathy. METHODS: This retrospective, observational study included patients with and without a diagnosis of CRS who underwent CT examination of the lungs between 2012 and 2014. Two radiologists, who were blinded for the presence of CRS, reviewed the scans for the presence of any abnormalities consensually. The χ(2) test was used for correlative analysis, with a significance level of 0.05. RESULTS: A total of 123 CT series (51.2% from male patients, mean age 41 ± 16 years) were reviewed, including those from 59 (48%) patients with a diagnosis of CRS. Patients with CRS were more likely than the control group to exhibit atelectasis, bronchiolectasis, centrilobular nodules and ground-glass opacities (all p < 0.05), with a significant predilection for middle lobe and lingular involvement observed (p < 0.001). Other abnormalities, such as bronchial wall thickening and air trapping, did not differ between groups. CONCLUSION: Atelectatic changes, ground-glass opacities, bronchiolectasis and centrilobular nodules are the most frequent abnormalities associated with CRS, with peculiar middle lobe and lingular involvement observed on chest CT examinations. ADVANCES IN KNOWLEDGE: CRS is a frequent disorder that displays typical pulmonary changes at CT. The recognition of such findings can prevent patients with this condition from undergoing unnecessary investigations that might be based on the presence of the aforementioned radiological features.

Ectopic Intrathoracic Kidney Presenting as Recurrent Pneumonias in a 1-year-old Infant: A Case Report.

Ectopic intrathoracic kidney is a rare congenital anomaly, representing less than 5% of all renal ectopias. Most cases are discovered in asymptomatic adult patients undergoing imaging exams for unrelated reasons. Less than twenty cases of thoracic kidneys in the infant group have been reported in the literature, mostly comprising asymptomatic patients. Herein, we report a case of an 18-month-old boy with recurrent pneumonia episodes who was found to have a right-sided intrathoracic ectopic kidney. A brief literature review addressing the pathogenesis, prognosis, and treatment of this condition is also presented.

Interobserver agreement between radiologists and radiology residents and emergency physicians in the detection of PE using CTPA.

OBJECTIVE: To assess interobserver agreement between thoracic radiologists, radiology residents, and emergency physicians in diagnosing pulmonary embolism (PE). MATERIALS AND METHODS: Emergency physicians, radiology residents, and thoracic radiologists evaluated 123 computed tomography pulmonary angiography images. Interobserver agreement was analysed using kappa statistics. RESULTS: Very good agreements were observed between thoracic radiologists and radiology residents (0.81 and 0.82). Fair and moderate agreements (0.39 and 0.42) were demonstrated between emergency physicians and thoracic radiologists. CONCLUSIONS: Important differences in interobserver agreement were found, with emergency physicians tending to overdiagnose PE.

Normal variance in emphysema index measurements in 64 multidetector-row computed tomography.

The purpose of this study was to identify the normal variance of emphysema index (EI) measured in examinations acquired with 64 multidetector-row computed tomography (64-MDCT). A longitudinal, noninterventional study was performed retrieving all patients in our institution who are currently registered in our lung nodule protocol. All patients with clinical, functional, or significant radiological changes were excluded. We assumed that EI should remain unchanged within a short period of time. We reviewed 475 MDCTs in order to select 50 clinically stable patients who had two sequential chest MDCTs performed within a time interval of less than three months, and who presented at least one lung free of abnormalities but emphysema. CT densitovolumetry was used to calculate EI with thresholds set at -950 Hounsfield units (HUs) (EI-950) and -970 HUs (EI-970); on both studies from each patient. We observed the variation of total lung volume (TLV), mean lung density (MDL), and EI for measurements at the baseline and at follow-up scans. Differences observed between baseline and follow-up measurements were: TLV µ= 149 ml; IC = µ +1.96 (133); EI-950 µ = 0.02%; p 95 = 0.89%; EI-970 µ = 0.04%; p 95 = 0.23% and MLD µ = 15 HU; IC = µ +1.96 (18). The correlations obtained were the following: TLV r = 0.96, EI-950 r = 0.79, EI-970 r = 0.85. Accepting that emphysema would remain unchanged within three months on stable patients, differences of less than 0.89% for EI-950 and of less than 0.23% for EI-970 are within the variance of the method.

On-line prediction of the feeding phase in high-cell density cultivation of rE. coli using constructive neural networks.

Streptococcus pneumoniae (pneumococcus) is a bacterium responsible for a wide spectrum of illnesses. The surface of the bacterium consists of three distinctive membranes: plasmatic, cellular and the polysaccharide (PS) capsule. PS capsules may mediate several biological processes, particularly invasive infections of human beings. Prevention against pneumococcal related illnesses can be provided by vaccines. There is a sound investment worldwide in the investigation of a proteic antigen as a possible alternative to pneumococcal vaccines based exclusively on PS. A few proteins which are part of the membrane of the pneumococcus seem to have antigen potential to be part of a vaccine, particularly the PspA. A vital aspect in the production of the intended conjugate pneumococcal vaccine is the efficient production (in industrial scale) of both, the chosen PS serotypes as well as the PspA protein. Growing recombinant Escherichia coli (rE. coli) in high-cell density cultures (HCDC) under a fed-batch regime requires a refined continuous control over various process variables where the on-line prediction of the feeding phase is of particular relevance and one of the focuses of this paper. The viability of an on-line monitoring software system, based on constructive neural networks (CoNN), for automatically detecting the time to start the fed-phase of a HCDC of rE. coli that contains a plasmid used for PspA expression is investigated. The paper describes the data and methodology used for training five different types of CoNNs, four of them suitable for classification tasks and one suitable for regression tasks, aiming at comparatively investigate both approaches. Results of software simulations implementing five CoNN algorithms as well as conventional neural networks (FFNN), decision trees (DT) and support vector machines (SVM) are also presented and discussed. A modified CasCor algorithm, implementing a data softening process, has shown to be an efficient candidate to be part of an on-line HCDC monitoring system for detecting the feeding phase of the HCDC process.

An innovative biocatalyst for production of ethanol from xylose in a continuous bioreactor.

The use of the hemicellulose fraction of biomass may be important for the feasibility of the production of second generation bioethanol. Wild strains of Saccharomyces cerevisiae are widely used in industry for production of 1st generation ethanol, and the robustness of this yeast is an important advantage in large scale applications. Isomerization of xylose to xylulose is an essential step in this process. This reaction is catalyzed by glucose isomerase (GI). A new biocatalyst is presented here for the simultaneous isomerization and fermentation (SIF) of xylose. GI from Streptomyces rubiginosus was immobilized in chitosan, through crosslinking with glutaraldehyde, and the support containing the immobilized GI (IGI-Ch) was co-immobilized with S. cerevisiae, in calcium alginate gel. The immobilization experiments led to high immobilized protein loads (30-68 mg × g(support)(-1)), high yields (circa of 100%) and high recovered enzyme activity (>90%). The IGI-Ch derivative with maximum activity presented 1700 IU × g(catalyst)(-1), almost twice the activity of a commercial immobilized GI, GENSWEET(®) IGI-HF. At typical operational conditions for xylose SIF operation (pH 5, 30-35 °C, presence of nutrients and ethanol concentrations in the medium up to 70 L(-1)), both derivatives, IGI-Ch and GENSWEET(®) IGI-HF retained app. 90% of the initial activity after 120 h, while soluble GI was almost completely inactive at pH 5, 30 °C. The isomerization xylose/xylulose, catalyzed by IGI-Ch, reached the equilibrium in batch experiments after 4h, with 12,000 IU × L(-1) (7 g(der) × L(-1)), at pH 5 and 30 °C, in the presence of fermentation nutrients. After co-immobilization of IGI-Ch with yeast in alginate gel, this biocatalyst succeeded in producing 12 g × L(-1) of ethanol, 9.5 g × L(-1) of xylitol, 2.5 g × L(-1) of glycerol and 1.9 g × L(-1) of acetate after consumption of 50 g × L(-1) of xylose, in 48 h, using 32.5 × 10(3) IU × L(-1) and 20 g(yeast) × L(-1), at 35 °C and initial pH 5.3.

In vitro synergisms obtained by amphotericin B and voriconazole associated with non-antifungal agents against Fusarium spp.

Fusarium spp is an opportunistic fungal pathogen responsible for causing invasive hyalohyphomycosis in immunocompromised patients. Due to its susceptibility pattern with a remarkable resistance to antifungal agents the treatment failures and mortality rates are high. To overcome this situation, combination therapy may be considered which must be subjected to in vitro tests. In vitro activities of amphotericin B, itraconazole, and voriconazole associated with azithromycin, ciprofloxacin, fluvastatin, ibuprofen, metronidazole, and also the combination of amphotericin B plus rifampin against 23 strains of Fusarium spp. through the checkerboard technique based on M38-A2 [Clinical and Laboratory Standards Institute (2008). Reference method for broth dilution antifungal susceptibility testing of filamentous fungi; approved standard, 2nd ed. (CLSI document M38-A2) (ISBN 1-56238-668-9). Wayne, PA: CLSI] were evaluated. The best synergistic interactions with amphotericin B were with ibuprofen (43.5%) (FICI [fractional inhibitory concentration index] range = 0.25-2). Combinations with voriconazole showed synergism, mainly with ciprofloxacin (30.4%) (FICI range = 0.25-3) and metronidazole (30.4%) (FICI range = 0.1-4); however, all the combinations with itraconazole were indifferent. In general, antagonistic interactions were not registered. Our results showed that in vitro synergisms obtained by some combinations studied deserve attention since they were better than those showed by the antimycotic.