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.

Adherence to anti-osteoporotic therapies: role and determinants of "spot therapy".

UNLABELLED: A successful therapy needs high level of adherence consisting in right drug intake in terms of persistence and compliance. Our study suggests adherence is higher if spot (less than 30 days) therapies are excluded; the analysis of spot therapy causes underlines the importance of the interpersonal aspects of medical practice. INTRODUCTION: A successful therapy needs a high level of adherence consisting in right drug intake in terms of persistence and compliance. The aim of this study was to evaluate anti-osteoporotic therapies recorded in general practitioner databases in the area of Rome, which used the same computerized medical record management. The study focused on evaluating therapy adherence, any adherence changes excluding spot therapies (less than 30 days), and any cause of early therapy discontinuation in a subgroup of patients randomly selected. METHODS: Thirty-one databases were evaluated, including a total of 6,390 anti-osteoporotic therapies: 5,853 were prescribed to women and 537 to men. The prescribed drugs were: vitamin D (13 %), calcium (8.7 %), vitamin D + calcium (40.1 %), raloxifene (3.3 %), alendronate (16.4 %), risedronate (7.7 %), clodronate (10.4 %), or other drugs (0.4 %). Spot therapies represented 53.7 % of the total prescriptions. The difference between adherence in the total group (24.64 %) and the group excluding spot therapies (43.38 %) is significant. The main factors influencing low adherence were side effects (27 %), misinformation given by the physician (17 %), insufficient motivation (9 %), difficult intake (9 %), and no perceived benefits (9 %). RESULTS: Our study suggests adherence is high and similar to other chronic diseases if spot therapies are excluded. The analysis of spot therapy causes suggests that an important role is played by the physician and the interpersonal aspects of medical practice, especially at the first prescriptions. CONCLUSIONS: The physician should collaborate with patients in choosing a personalized medical treatment. Reducing spot therapy could be the real goal in order to improve anti-osteoporotic therapy adherence.

ηπ+ π- resonant structure around 1.8 GeV/c(2) and η(1405) in J/ψ → ωηπ+ π-.

We present results of a study of the decay J/ψ → ωηπ+ π- using a sample of (225.2 ± 2.8) × 10(6) J/ψ events collected by the BESIII detector, and report the observation of a new process J/ψ → ωX(1870) with a statistical significance of 7.2σ, in which X(1870) decays to a(0)(±)(980)π±. Fitting to ηπ+ π- mass spectrum yields a mass M = 1877.3 ± 6.3(stat)(-7.4)(+3.4)(syst) MeV/c(2), a width Γ = 57 ± 12(stat)(-4)(+19)(syst) MeV/c(2), and a product branching fraction B(J/ψ → ωX) × B(X→a(0)(±)(980)π±) × B(a(0) (±)(980) → ηπ±) = [1.50 ± 0.26(stat)(-0.36)(+0.72) (syst)] × 10(-4). Signals for J/ψ → ωf(1)(1285) and J/ψ → ω η(1405) are also clearly observed and measured.

Observation of χ(c1) decays into vector meson pairs φφ, ωω, and ωφ.

Using (106±4)×10⁻6 ψ(3686) events accumulated with the BESIII detector at the BEPCII e⁺e⁻ collider, we present the first measurement of decays of χ(c1) to vector meson pairs φφ, ωω, and ωφ. The branching fractions are measured to be (4.4±0.3±0.5)×10⁻4, (6.0±0.3±0.7)×10⁻4, and (2.2±0.6±0.2)×10⁻5, for χ(c1)→φφ, ωω, and ωφ, respectively, which indicates that the hadron helicity selection rule is significantly violated in χ(cJ) decays. In addition, the measurement of χ(cJ)→ωφ provides the first indication of the rate of doubly OZI-suppressed χ(cJ) decay. Finally, we present improved measurements for the branching fractions of χ(c0) and χ(c2) to vector meson pairs.

Confirmation of the X(1835) and observation of the resonances X(2120) and X(2370) in J/ψ→γπ+π-η'.

With a sample of (225.2±2.8)×10(6) J/ψ events registered in the BESIII detector, J/ψ→γπ(+)π(-)η(') is studied using two η(') decay modes: η(')→π(+)π(-)η and η(')→γρ(0). The X(1835), which was previously observed by BESII, is confirmed with a statistical significance that is larger than 20σ. In addition, in the π(+)π(-)η(') invariant-mass spectrum, the X(2120) and the X(2370), are observed with statistical significances larger than 7.2σ and 6.4σ, respectively. For the X(1835), the angular distribution of the radiative photon is consistent with expectations for a pseudoscalar.

Procutase versus 1% silver sulphadiazine in the treatment of minor burns.

The purpose of this randomised comparative study was to evaluate the use of silver sulphadiazine (SSD) 1% cream (Group A) with the use of Procutase (Group B) in treating burns with a TBSA <10% and a depth not greater than 2nd degree burns and thus suitable for outpatient management. The two groups were similar in age, gender, race, and extent of burn. Procutase is an ionic hydrogel composed of natural hydrophilic polymers in an active ionic solution with an inhibitor of matrix metalloproteinases MMP-1, -3 and -9 (collagenase/gelatinase). Subjects were seen in follow-up biweekly, and wounds of patients in SSD group were compared with those of Procutase group for healing time, pain score at dressing change, compliance with therapy and complication rate. The result of this study showed that Procutase treated patients had statistically significantly less pain and shorter wound healing time. Procutase can be used successfully in patients with burns that do not require hospital admission.

Evidence for ψ' decays into γπ0 and γη.

The decays ψ'→γπ(0), γη and γη' are studied using data collected with the BESIII detector at the BEPCII e(+)e(-) collider. The processes ψ'→γπ(0) and ψ'→γη are observed for the first time with signal significances of 4.6σ and 4.3σ, respectively. The branching fractions are determined to be B(ψ'→γπ(0))=(1.58±0.40±0.13)×10(-6), B(ψ'→γη)=(1.38±0.48±0.09)×10(-6), and B(ψ'→γη')=(126±3±8)×10(-6), where the first errors are statistical and the second ones systematic.

Do hypertension and diabetes mellitus influence the site of atherosclerotic plaques?

BACKGROUND: The concomitant occurrence of atherosclerotic plaques in carotid, coronary and peripheral vessels has been described in a number of studies. A few studies were, on the contrary, done for determining the role of hypertension and/or type 2 diabetes mellitus for the occurrence of the atherosclerotic plaques in different anatomical sites. Moreover these studies deal with atherosclerotic lesions that are generally considered, without differentiating their morphology as a function of the underlying disease, territory, and risk factors. Primary aim of this study is, thus, to verify whether the two most common causes for atherosclerotic disease, i.e., hypertension and type 2 diabetes mellitus, may influence the site of appearance of the atherosclerotic plaque. A second aim is to verify if the anatomical site of the plaque influences plaque morphology and vulnerability. PATIENTS AND METHODS: A retrospective study of 244 patients affected with type 2 diabetes mellitus or hypertension was performed; 114 subjects were affected by moderate-severe and drugs-treated hypertension (Group A); 55 were affected by type 2 diabetes mellitus in treatment with oral antidiabetic drugs (Group B); 75 were diagnosed as affected by the association hypertension and diabetes (Group C). The inclusion criteria were: exhaustive images of the cardiovascular system (coronary angiography, colour Doppler ultrasound of lower limb arteries and carotid arteries, transthoracic Doppler echocardiography ) and a serum lipid profile (total serum cholesterol, HDL-cholesterol, LDL-cholesterol, triglycerides). Three different anatomical sites: carotid axis, ilio-femoral arteries and coronary district, were considered. In each site a plaque lesion-classification was performed to describe the morphology of the plaque. RESULTS: In patients with hypertension, carotid district seems to be the preferential site of onset of atherosclerotic plaques even if a statistical significant association between the two conditions was not found. Statistical evaluation didn't show significant association between different risk factors and coronary district too. On the opposite, a significant association (p < 0.001) between diabetes and the presence of atherosclerotic plaques into lower limb district was found. A very significant association (p < 0.001) between type 2-diabetes and the presence of non-ulcerative plaques was found too. CONCLUSIONS: Our study underlines the relationship between vessel plaques localization and concomitant risk factors for atherosclerosis and suggests a possible difference in plaque morphology and biological behaviour related to different anatomical site.

Common mechanisms for pathogens of plants and animals.

The vast evolutionary gulf between plants and animals--in terms of structure, composition, and many environmental factors--would seem to preclude the possibility that these organisms could act as receptive hosts to the same microorganism. However, some pathogens are capable of establishing themselves and thriving in members of both the plant and animal kingdoms. The identification of functionally conserved virulence mechanisms required to infect hosts of divergent evolutionary origins demonstrates the remarkable conservation in some of the underlying virulence mechanisms of pathogenesis and is changing researchers' thinking about the evolution of microbial pathogenesis.

A rolling-circle miniplasmid of Xanthomonas campestris pv. glycines: the nucleotide sequence and its use as a cloning vector.

The indigenous multicopy miniplasmid (pXG33) of Xanthomonas campestris pv. glycines was entirely sequenced and evaluated as a cloning vector for Xanthomonas. The pXG33 contains 1738 bp and the nucleotide sequence revealed a consensus nicking site (TGATA) described for the pC194 family of rolling-circle replicating (RCR) plasmids. This nicking site is embebbed in a region of high potential to form a number of stem-loop structures. The predicted protein (Rep) showed conserved amino acid residues and potential catalytic regions, containing conserved Tyr and Glu residues. These results indicate that pXG33 replicates by a rolling-circle mechanism. For use as a cloning vector for Xanthomonas, a fragment containing the kanamycin resistance gene (aphA) and the stabilization locus (parB) was inserted into pXG33. The new construct, of 3.4 kb, was designated pXG31. By deletion of the parB locus and using pBluescript KS(+) as an intermediate, pXG40 (2.8 kb), containing unique restriction sites for BamHI, EcoRI, SacI, and KpnI at the ends of the kanamycin resistance gene, was generated. Both constructs showed stability in Xanthomonas during 18 h of growth or 72 h of fermentation, high-copy number, and no interference with pathogenicity. pXG31 and pXG40, however, were incapable of duplication in Escherichia coli and a shuttle vector (pKX33) was constructed by inactivation of some restriction sites of pXG40 and ligation to the cloning vector pBluescript KS(+). pKX33 is nonconjugative, is multicopy, is of low molecular weight (5.7 kb), presents antibiotic resistance markers for ampicillin and kanamycin, has unique restriction sites for KpnI, SalI, EcoRV, EcoRI, BamHI, XbaI, and SacI, and can be used directly for sequencing with universal primers. It can be maintained in E. coli and several species and pathovars of Xanthomonas.

The CIRCE element and its putative repressor control cell cycle expression of the Caulobacter crescentus groESL operon.

The groESL operon is under complex regulation in Caulobacter crescentus. In addition to strong induction after exposure to heat shock, under physiological growth conditions, its expression is subject to cell cycle control. Transcription and translation of the groE genes occur primarily in predivisional cells, with very low levels of expression in stalked cells. The regulatory region of groESL contains both a sigma32-like promoter and a CIRCE element. Overexpression of C. crescentus sigma32 gives rise to higher levels of GroEL and increased levels of the groESL transcript coming from the sigma32-like promoter. Site-directed mutagenesis in CIRCE has indicated a negative role for this cis-acting element in the expression of groESL only at normal growth temperatures, with a minor effect on heat shock induction. Furthermore, groESL-lacZ transcription fusions carrying mutations in CIRCE are no longer cell cycle regulated. Analysis of an hrcA null strain, carrying a disruption in the gene encoding the putative repressor that binds to the CIRCE element, shows constitutive synthesis of GroEL throughout the Caulobacter cell cycle. These results indicate a negative role for the hrcA gene product and the CIRCE element in the temporal control of the groESL operon.

Identification of a Caulobacter crescentus operon encoding hrcA, involved in negatively regulating heat-inducible transcription, and the chaperone gene grpE.

In response to elevated temperature, both prokaryotic and eukaryotic cells increase expression of a small family of chaperones. The regulatory network that functions to control the transcription of the heat shock genes in bacteria includes unique structural motifs in the promoter region of these genes and the expression of alternate sigma factors. One of the conserved structural motifs, the inverted repeat CIRCE element, is found in the 5' region of many heat shock operons, including the Caulobacter crescentus groESL operon. We report the identification of another C. crescentus heat shock operon containing two genes, hrcA (hrc for heat shock regulation at CIRCE elements) and a grpE homolog. Disruption of the hrcA gene, homologs of which are also found upstream of grpE in other bacteria, increased transcription of the groESL operon, and this effect was dependent on the presence of an intact CIRCE element. This suggests a role for HrcA in negative regulation of heat shock gene expression. We identified a major promoter transcribing both hrcA and grpE and a minor promoter located within the hrcA coding sequence just upstream of grpE. Both promoters were heat shock inducible, with maximal expression 10 to 20 min after heat shock. Both promoters were also expressed constitutively throughout the cell cycle under physiological conditions. C. crescentus GrpE, shown to be essential for viability at low and high temperatures, complemented an Escherichia coli delta grpE strain in spite of significant differences in the N- and C-terminal regions of these two proteins, demonstrating functional conservation of this important stress protein.

[Color Doppler echography in the study of obstruction-related lung collapse]. / L'eco color Doppler nello studio delle atelettasie polmonari su base ostruttiva.

The typical US pattern of obstructive atelectasis consists in a triangular hypoechoic area with anechoic bands inside related to fluid-filled bronchial structures--the US fluid bronchogram sign. According to some authors, this US sign within a chest mass indicates pulmonary parenchyma disease. Furthermore, it suggests the diagnosis of lung collapse. Sixty-one patients with obstructive atelectasis confirmed with conventional radiography, conventional and computed tomography, and bronchoscopy were submitted to B-mode and color-Doppler US to assess the importance of the US fluid bronchogram sign in obstructive pulmonary atelectasis. In this condition, B-mode US showed tubular anechoic bands in 59/61 patients. Power Doppler venous sampling showed a Doppler spectrum with marked phase oscillations. Arterial sampling showed a Doppler spectrum with high distal impedance-with poor or totally absent diastolic component. To conclude, in the atelectasis area, B-mode US showed in 96% of patients some anechoic bands with no apparent pulsatility. Color-Doppler showed color flow in 100% of cases, which confirmed the vascular nature of the masses. Thus, the US fluid bronchogram, which is frequently described in the literature, was never observed in our series. Power Doppler spectral flow analysis can be useful in the diagnosis of obstructive atelectasis because it depicts the hemodynamics of atelectasis parenchyma. Indeed, the arterial spectrum with high distal resistance is consistent with the effects of hypoxia on intra-atelectatic blood vessels. Further research is necessary to assess the role of color-Doppler US in the hemodynamic study of intra-atelectatic vessels. However, our preliminary results open new perspectives for the acquisition of physiopathologic data on abnormal blood flow in obstructive atelectasis.