Predicting the reactivity of proteins from their sequence alone: Kazal family of protein inhibitors of serine proteinases

An additivity-based sequence to reactivity algorithm for the interaction of members of the Kazal family of protein inhibitors with six selected serine proteinases is described. Ten consensus variable contact positions in the inhibitor were identified, and the 19 possible variants at each of these positions were expressed. The free energies of interaction of these variants and the wild type were measured. For an additive system, this data set allows for the calculation of all possible sequences, subject to some restrictions. The algorithm was extensively tested. It is exceptionally fast so that all possible sequences can be predicted. The strongest, the most specific possible, and the least specific inhibitors were designed, and an evolutionary problem was solved.

Synthesis, characterization, and X-ray crystal structures of Co(II) and La(III) complexes of a pyridine containing self-assembling system and solution studies of the Co(II) complex

The complexes [pyda.H]2[Co(pydc)2]·H2O (I) and [pyda·H]2[La2(pydc)4(H2O)4].2H2O (II) were prepared from the complexation of a novel pyridine containing self-assembling system LH2, ([pyda·H2]2+[pydc]2–) (pyda = 2,6-pyridinediamine and pydc·H2 = 2,6-pyridinedicarboxylic acid), with cobalt(II) and lanthanum(III) salts in 82% and 74% yields, respectively. The characterizations were performed using elemental analysis, ESI mass spectroscopy as well as 1H and 13C solution NMR spectroscopy, and X-ray crystallography. The crystal systems I and II are monoclinic and triclinic with space groups P21/n and P[Formula: see text] respectively. Coordination number around each Co atom is six with distorted octahedral geometry, while coordination number around each La atom is nine with highly distorted tricapped trigonal prism geometry. The paramagnetic Co(II) and diamagnetic La(III) complexes show 1H NMR resonances of both anionic [pydc]2- and cationic counter ion [pyda·H]+ in DMSO-d6. The complexation reactions of the complex I in aqueous solution were investigated by potentiometric pH titrations and the equilibrium constants for all major complexes formed are described. The results are presented in the form of distribution diagrams revealing the concentrations of individual complex species as a function of pH. The results revealed that at a pH range 4.0–4.5 the major complex species is [(pyda·H)]2[Co(pydc)2].Key words: self-assembly, X-ray crystal structure, Co(II) complex, La(III) complex, 2,6- pyridinedicarboxylic acid, 2,6-pyridinediamine, hydrogen bonding.

TLR4 polymorphism in Iranian patients with brucellosis

OBJECTIVE

Brucellosis is a zoonosis of both public health and economic significance in most developing countries. Polymorphisms in Toll-like receptor-4 (TLR4) have been reported to be associated with a blunted immune response to microbial pathogens. Information regarding any association between genetic variation of TLR4 and susceptibility to brucellosis is not available in the literatures. The main purpose of this research is to evaluate the role of polymorphic alleles of TLR4 gene in susceptibility to brucellosis.

MATERIALS AND METHODS

In this case-control study, 198 patients with brucellosis and 111 healthy volunteers matched for sex, age and geographic area were evaluated by genotyping for polymorphism in TLR4 gene (Asp299Gly) using amplification refractory mutation system (ARMS)-PCR method.

RESULTS

Allele 896G was more prevalent in patients with brucellosis compared to healthy controls (33.6% vs. 20.7%, P=0.000003). Also the frequency of G allele of TLR4 gene was significantly higher in male patients with brucellosis compared to the same sex in control group (36% vs. 21.7%, P=0.00005). Multiple logistic regression analysis demonstrated that male patients heterozygous at allele G gene had a significantly higher risk for brucellosis with an odds ratio of OR 2.89, 95% CI: 1.79-4.69, P<0.0001).

CONCLUSION

This study is the first to show an association between genetic polymorphism in TLR4 gene and susceptibility to brucellosis.

Protective effects of sodium nitrate against testicular apoptosis and spermatogenesis impairments in streptozotocin-induced diabetic male rats

AIMS

As nitric oxide (NO) production is essential for insulin signaling, glucose uptake, endothelial function, and regulation of apoptosis, the loss of bioavailable NO may be a mechanism underlying the development of diabetes complication. Dietary nitrate acts as a substrate for NO generation, thus serving as a physiological source of NO. This study evaluated the therapeutic effects of nitrate supplementation on the apoptosis-induced testicular disorders in diabetic rats.

MAIN METHODS

Fifty male Wistar rats were divided into five groups; control, control with 100 mg/L nitrate in distilled drinking water, diabetes, diabetes treated with 2-4 U/day NPH insulin, diabetes treated with 100 mg/L nitrate in distilled drinking water. After 8 weeks, blood samples, testis, and epididymis were collected to assess the apoptosis process and the stereology of testis tissue, sperm motility, morphology and DNA fragmentation, and also mRNA expression of miR-449a, p53, Pdcd4, and Pacs2 mRNA, as well as serum glucose, insulin, and NOx levels were investigated.

KEY FINDINGS

The results of this study indicated that nitrate treatment ameliorated the sperm parameters, testicular morphometrical and stereological alterations, reduced blood glucose, the number of TUNEL positive cells and tubules, and testicular expressions of p53, Pdcd4, and Pacs2 mRNA as well as increased body weight, serum insulin and NOx levels, and testicular expression of miR-449a in streptozotocin-induced diabetic rats.

SIGNIFICANCE

Our in vivo evidence revealed that nitrate treatment may has a favorable effect as an exogenous NO donor on experimental diabetic testicular damages in which NO bioavailability is impaired.

Evaluation of choroidal substructure perfusion in patients affected by systemic sclerosis: an optical coherence tomography angiography study

Objective: Vasculopathy in systemic sclerosis (SSc) is characterized by the obliteration of arterioles and a reduced capillary density in various tissues. In SSc, atrophic alterations of the choroid have been suggested based on morphological data acquired by optical coherence tomography (OCT). In this study, we aimed to assess the choroid in eyes of patients with SSc from a microcirculatory, dynamic point of view by adding optical coherence tomography angiography (OCTA) to the diagnostic spectrum.Method: SSc patients were enrolled, and age- and gender-matched healthy subjects were used as controls. In addition to basic ophthalmological and rheumatological examinations, individuals underwent enhanced-depth imaging OCT and OCTA. Subfoveal thicknesses of the choroid as well as all three choroidal vascular sublayers were measured and submacular perfusion values were evaluated.Results: In total, 12 patients with SSc and 12 matched controls were included. The median age of participants was 64 years. Submacular perfusion was significantly lower in the choriocapillaris (Δ = 0.72%; p = 0.045), Sattler's layer (Δ = 2.87%; p = 0.001), and Haller's layer (Δ = 2.69%; p = 0.018) of SSc patients compared to controls. Subfoveal thicknesses of Sattler's layer (Δ = 15 µm; p = 0.026) and Haller's layer (Δ = 41 µm; p = 0.045) were also significantly smaller in the SSc group.Conclusion: Choroidal microcirculation is impaired in SSc, even in patients without ophthalmological symptoms. Choroidal OCT and OCTA may offer additional biomarkers for SSc activity.

Epithelial-mesenchymal transition process during embryo implantation

The epithelial to mesenchymal transition (EMT) in endometrial epithelial and trophectoderm cells is essential for the progression of embryo implantation and its impairment could cause implantation failure. Therefore, EMT should be tightly regulated in both embryonic and endometrial cells during implantation. Studies reported the involvement of numerous factors in EMT regulation, including hormones, growth factors, transcription factors, microRNAs, aquaporins (AQPs), and ion channels. These factors act through different signaling pathways to affect the expression of epithelial and mesenchymal markers as well as the cellular cytoskeleton. Although the mechanisms involved in cancer cell EMT have been well studied, little is known about EMT during embryo implantation. Therefore, we comprehensively reviewed different factors that regulate the EMT, a key event required for the conceptus implantation to the endometrium.Summary sentence: Abnormal epithelial-mesenchymal transition (EMT) process within endometrial epithelial cells (EECs) or trophoblast cells can cause implantation failure. This process is regulated by various factors. Thus, the objective of this review was to summarize the effective factors on the EMT process during implantation.

Synthesis, NMR Characterisation, X–ray Crystal Structure and Solution Studies of Ni(II) Complexes of a Pyridine Containing Self–assembling System

X-ray analysis of Ni(II) complexes of the self-assembling system LH2, [pyda.H2][pydc] (pydc.H2 = 2,6-pyridinedicarboxylic acid and pyda = 2,6-pyridinediamine), indicated that two six-coordinated anionic [pyda.H]2[Ni(pydc)2].H2O (I) and neutral [Ni(pydc.H)2].3H2O (II) complexes are formed at different temperature conditions in water; in agreement with the results obtained from potentiometric pH titrations in the pH range 3.5–5.5.

Improvement of Medium And Light Oil Recovery With Thermocatalytic In Situ Combustion

Abstract

The objective of this paper was to improve the understanding of the basic mechanisms responsible for fuel formation in in situ combustion (ISC) and to use that understanding to identify the conditions under which the ISC process can be applied to improve the recovery of heavy, medium and light oils. Using rocks of varying mineralogical composition and crude oils with different contents of asphalteoes and resins, pyrolysis and combustion tests were performed to examine the influence of thermocatalytic mocatalytic reactions on the amount and reactivity of fuel in an ISC process.

From the results, it appears that the controlling mechanism of fuel formation is the conversion of crude oil components by radical polymerization. The conversion rate is influenced by many factors such as process condition and the nature of the crude oil and reservoir rock minerals. The formation of resins from lighter hydrocarbons and their polymerization into asphalrenes can be accelerated by clay minerals and metal components existing in the fuel formation zone. Therefore the importance of low tem-perature oxidation reactions is increasing in the thermocatalytic recovery process of even light and medium oils.

Introduction

The application of thermal energy to hydrocarbon reservoirs for increasing crude oil recovery has been given much attention. There are two main types of thermal recovery process, namely hot fluid injection and in situ combustion (ISC). ISC is thermal oil recovery method with a large theoretical potential but limited success in field application. This technique is also known to be the most complicated oil recovery method. It includes some aspects of nearly every oil recovery process.

An important parameter to be considered in the design of an ISC project is the amount of fuel deposited ahead of the combustion front. Excessive fuel deposition causes a slow rate of advance of the burning front and large air compression costs and reduces the maximum oil recovery. On the other hand, if the fuel concentration is too low, the heat of combustion will not be sufficient to raise the temperature of the rock and the contained fluids to a level of self-sustained combustion. This leads to an unstable burning front and combustion failure. Thus, it is necessary to understand the reactions occurring at different temperatures as the combustion front moves in the reservoir.

The most important controlling factors of the fuel formation are the nature of the crude oil and reservoir rock minerals and During this work, experiments were conducted to describe how the clay minerals and heavy metals derivatives, such as iron, affect the thermocatalytic conversion of crude oil compounds as well as the fuel formation and combustion.

Thermocatalytic Oxidation of Crude Oil Compounds

It has been confirmed by many authors, for example, Bousaid and Ramey(3), Dabous and Fulton(4) Burger and Sahuquet(5), that basically three major reactions occur at different temperature levels in an ISC process. These reactions are known as:Low temperature oxidation (LTO)Fuel deposition reactions (FDR)High temperature oxidation (HTO)

Monitoring of the therapeutic efficacy of chloroquine for the treatment of uncomplicated,Plasmodium falciparummalaria in Iran

Between 2002 and 2004, the standardized 28-day protocol recently developed by the World Health Organization was used to explore the efficacy of chloroquine, in the treatment of uncomplicated, Plasmodium falciparum malaria, in five sentinel sites in southern Iran. All but 14 of the 158 patients enrolled (128, 28 and two from the provinces of Sistan-Baluchestan, Hormozgan and Kerman, respectively) were successfully followed-up. The overall frequency of treatment failure by day 28 was 78.5%, with 17.4% of the patients being classed as early treatment failures, 34.7% as late clinical failures, and 26.4% as late parasitological failures. There appeared to be no significant change in the frequency of treatment failure between the 2002-2003 and 2003-2004 transmission seasons, nor any significant between-site variation in the efficacy of chloroquine. Given these observations, the replacement of chloroquine, as the first-line drug for the treatment of uncomplicated, P. falciparum malaria in Iran, was inevitable. Artesunate-sulfadoxine-pyrimethamine is now the recommended first-line treatment, with artemether-lumefantrine used for second-line treatment. The efficacies of these combination therapies are currently being evaluated and monitored.

Lessons learnt from malaria epidemics in the Islamic Republic of Iran

The Islamic Republic of Iran is in the pre-elimination phase of malaria control, but malaria epidemics are still a concern in the south of the country. This retrospective study presents the epidemiological characteristics and predisposing factors of 60 of the malaria epidemics reported in Sistan va Baluchestan province during 2005-09. A zero-truncated negative binomial model was used to investigate the relation between predictor variables and the total number of malaria cases. Malaria epidemics occurred mainly in the southern part of the province, mostly between July and October, peaking in August. Most malaria epidemics were small-scale (68.3% were < 100 cases) and short (51.7% lasted < 1 month). Plasmodium falciparum was present in 46.7% of the epidemics. An increase in the rainfall rate as well as population movements were the most significant predisposing factors. The results may help inform an epidemic investigation and reporting system as the country approaches the malaria elimination phase.

Certain haplotypes of the 3'-UTR region of the HLA-G gene are linked to breast cancer

Background: Human leukocyte antigen G belongs to the family of non-classical HLA class I genes, its expression considered an important immune escape mechanism of cancer cells. The polymorphisms in the 3'-untranslated region (UTR) region of HLA-G influence the magnitude of the protein by modulating HLA-G mRNA stability. We hypothesised links between any of eight (UTR) single nucleotide polymorphisms (SNPs) and their haplotype of the HLA-G gene with breast cancer. Materials and Methods: Peripheral blood DNA from 100 patients affected by breast cancer and 100 controls was PCR sequenced for genotyping of 25 HLA-G 3'-UTR regions, including rs371194629 (+2960), rs1707 (+3003), rs1710 (+3010), rs17179101 (+3027), rs1063320 (+3142), rs9380142 (+3187), rs1610696 (+3196), and rs1233331 (+3227). Results: The 14-bp deletion (p = 0.01), and the +3010 (p = 0.021), +3142 (p = 0.006) and +3187 (p = 0.046) variants were significantly more prevalent in patients than in controls. In combining these data, two haplotypes of all eight SNPs and deletion/insertion (UTR-1 and UTR-4) are associated with breast cancer. Conclusion: Certain variants in the 3-UTR, and their combination as a haplotype, of the HLA-G gene are linked to breast cancer.

A Systematic Review and Meta-analysis of the Effects of Music Therapy on Postpartum Anxiety and Pain Levels

Introduction: Postpartum anxiety may be associated with depression, postpartum blues, and maternal mood disorders. This systematic review investigated the effects of music therapy on postpartum anxiety and pain levels.

Methods: English databases including Cochrane, Medline, Embase, Web of Science, Scopus, and PubMed and Persian databases including Scientific Information Database (SID) and the Iranian Registry of Clinical Trials (IRCT) were searched. The data were analyzed in RevMan 5.3 and reported as forest plots. The present study was conducted on postpartum women (i.e., the participants). All randomized controlled trials comparing the effects of music (i.e., the intervention) and placebo or routine care (i.e., the control) on postpartum anxiety and pain (i.e., the outcome) were included in the study.

Results: Out of a total of 60 retrieved articles, four eligible articles were selected and entered the meta-analysis process. According to the results, anxiety (MD=-0.68, 95% CI=-1.90 to -0.54, P < 0.001) and pain (MD=-1.85, 95% CI=-3.96 to 0.26, P < 0.001) levels of patients in the music therapy group were reduced more significantly than those in the control group.

Conclusion: The results showed that music therapy can significantly reduce both postpartum anxiety and pain scores. However, due to the high heterogeneity of the studies, more randomized trials using a standard tool such as the Consolidated Standards of Reporting Trials (CONSORT) statement are needed.

The interleukin-1 family gene polymorphisms and Graves' disease

Genetic factors, including cytokine gene polymorphisms, are potential contributors to the pathogenesis of the Graves' disease (GD). We attempted in this study to determine the association between GD and the following polymorphisms in the interleukin-1 (IL-1) family genes: IL-1alpha (-889C/T), IL-1ss (-511C/T), IL-1ss (+3962C/T), IL-1R (Pst-1 1970C/T) and IL-1RA (Mspa-I 11100C/T). We studied 107 patients with an established diagnosis of GD and 140 healthy controls. Cytokine typing was performed by the polymerase chain reaction with sequence-specific primers assay. Genotype distributions among patients were in Hardy-Weinberg equilibrium for all polymorphisms. The frequency of the IL-1alpha -889T allele was significantly higher in patients than in controls (51.9% vs. 31.6%, OR=2.33, 95% CI=1.61-3.38; p<0.0001). The IL-1RA Msp-I 11100C allele was significantly more frequent in patients than in controls (50.0% vs. 22.9%, OR=3.38, 95% CI=2.29-4.97, p<0.0001). No significant associations were found for other polymorphisms. Although the IL-1 family has well-known roles in GD pathogenesis, the contributions of their genetic variations to the disease are unclear. In this study, we documented a highly significant association between GD and polymorphism in IL-1alpha and IL-1RA genes. Further studies in other populations are necessary to confirm our results.

Development and prospective in-patient proof-of-concept validation of a surface photogrammetry + CT-based volumetric motion model for lung radiotherapy

PURPOSE

We develop and validate a motion model that uses real-time surface photogrammetry acquired concurrently with four-dimensional computed tomography (4DCT) to estimate respiration-induced changes within the entire irradiated volume, over arbitrarily many respiratory cycles.

METHODS

A research, couch-mounted, VisionRT (VRT) system was used to acquire optical surface data (15 Hz, ROI = 15 × 20 cm² ) from the thoraco-abdominal surface of a consented lung SBRT patient, concurrently with their standard-of-care 4DCT. The end-exhalation phase from the 4DCT was regarded as reference and for each remaining phase, deformation vector fields (DVFs) with respect to the reference phase were computed. To reduce dimensionality, the first two principal components (PCs) of the matrix of nine DVFs were calculated. In parallel, ten phase-averaged VRT surfaces were created. Surface DVFs and corresponding PCs were computed. A principal least squares regression was used to relate the PCs of surface DVF to those of volume DVFs, establishing a relationship between time-varying surface and the underlying time-varying volume. Proof-of-concept validation was performed during each treatment fraction by concurrently acquiring 30 s time series of real-time surface data and "ground truth" kV fluoroscopic data (FL). A ray-tracing algorithm was used to create a digitally reconstructed fluorograph (DRF), and motion trajectories of high-contrast, soft-tissue, anatomical features in the DRF were compared with those from kV FL.

RESULTS

For five of the six fluoroscopic acquisition sessions, the model out-performed 4DCT in predicting contour Dice coefficient with respect to fluoroscopy-derived contours. Similarly, the model exhibited a marked improvement over 4DCT for patch positions on the diaphragm. Model patch position errors varied from 5 to -15 mm while 4DCT errors ranged between 5 and -22.4 mm. For one fluoroscopic acquisition, a marked change in the a priori internal-external correlation resulted in model errors comparable to those of 4DCT.

CONCLUSIONS

We described the development and a proof-of-concept validation for a volumetric motion model that uses surface photogrammetry to correlate the time-varying thoraco-abdominal surface to the time-varying internal thoraco-abdominal volume. These early results indicate that the proposed approach can result in a marked improvement over 4DCT. While limited by the duration of the fluoroscopic acquisitions as well as the resolution of the acquired images, the DRF-based proof-of-concept technique developed here is model-agnostic, and therefore, has the potential to be used as an in-patient validation tool for other volumetric motion models.