Geometric approach to nonlinear coherent states using the Higgs model for harmonic oscillator

In this paper, we investigate the relation between the curvature of the physical space and the deformation function of the deformed oscillator algebra using non-linear coherent states approach. For this purpose, we study two-dimensional harmonic oscillators on the flat surface and on a sphere by applying the Higgs modell. With the use of their algebras, we show that the two-dimensional oscillator algebra on a surface can be considered as a deformed one-dimensional oscillator algebra where the effect of the curvature of the surface is appeared as a deformation function. We also show that the curvature of the physical space plays the role of deformation parameter. Then we construct the associated coherent states on the flat surface and on a sphere and compare their quantum statistical properties, including quadrature squeezing and antibunching effect.Comment: 12 pages, 7 figs. To be appeared in J. Phys.

OrganismTagger: detection, normalization and grounding of organism entities in biomedical documents

Motivation: Semantic tagging of organism mentions in full-text articles is an important part of literature mining and semantic enrichment solutions. Tagged organism mentions also play a pivotal role in disambiguating other entities in a text, such as proteins. A high-precision organism tagging system must be able to detect the numerous forms of organism mentions, including common names as well as the traditional taxonomic groups: genus, species and strains. In addition, such a system must resolve abbreviations and acronyms, assign the scientific name and if possible link the detected mention to the NCBI Taxonomy database for further semantic queries and literature navigation. Results: We present the OrganismTagger, a hybrid rule-based/machine learning system to extract organism mentions from the literature. It includes tools for automatically generating lexical and ontological resources from a copy of the NCBI Taxonomy database, thereby facilitating system updates by end users. Its novel ontology-based resources can also be reused in other semantic mining and linked data tasks. Each detected organism mention is normalized to a canonical name through the resolution of acronyms and abbreviations and subsequently grounded with an NCBI Taxonomy database ID. In particular, our system combines a novel machine-learning approach with rule-based and lexical methods for detecting strain mentions in documents. On our manually annotated OT corpus, the OrganismTagger achieves a precision of 95%, a recall of 94% and a grounding accuracy of 97.5%. On the manually annotated corpus of Linnaeus-100, the results show a precision of 99%, recall of 97% and grounding accuracy of 97.4%. Availability: The OrganismTagger, including supporting tools, resources, training data and manual annotations, as well as end user and developer documentation, is freely available under an open-source license at http://www.semanticsoftware.info/organism-tagger. Contact: [email protected]

Antibacterial Activity of Iranian Green and Black Tea on Streptococcus Mutans: An In Vitro Study

Objective: Dental caries is a common infectious disease.Streptococcus mutans is the prevalent decay microorganism. The anti Streptococcus mutans activity of non fermented and semi-fermented tea has been shown. The aim of this study was to determine the anti Streptococcus mutans activity of Iranian green and black tea (non fermented and fermented type).Materials and Methods: The study was experimental. The aerial parts of wild-growing Camellia sinensis were collected from Lahijan province. The methanolic extract of green and black tea were examined on Streptococcus mutans (ATCC3566). Five different concentrations (50mg/ml, 100mg/ml, 200mg/ml, 300mg/ml and 400 mg/ml) of tea extracts were tested using the well assay method. The agar dilution method recommended by the NCCLS standards (National Committee for Clinical Laboratory Standards) was used. Theminimum inhibitory concentration (MIC) was determined as the lowest concentration of extract inhibiting visible growth of the organism on the agar media plate. Minimum bactericidal concentration (MBC) was detected from MIC.Results: The Iranian green and black tea had an antibacterial effect on 100 to 400 mg/ml concentrations. The minimum inhibitory concentration of green and black tea was 150 and 50 mg/ml, respectively. The mean diameter of inhibition zone were 9.5 mm and 10.9 mm for methanolic extract of green and black tea, respectively.Conclusion: Both Iranian non fermented (green tea) and fermented (black tea) have anti Streptococcus mutans activity in vitro. The anti Streptococcus mutans activity of black tea appears on a lower concentration than green tea

Hinge Region in DNA Packaging Terminase pUL15 of Herpes Simplex Virus: A Potential Allosteric Target for Antiviral Drugs

Approximately 80% of adults are infected with a member of the herpesviridae family. Herpesviruses establish life-long latent infections within neurons, which may reactivate into lytic infections due to stress or immune suppression. There are nine human herpesviruses (HHV) posing health concerns from benign conditions to life threatening encephalitis, including cancers associated with viral infections. The current treatment options for most HHV conditions mainly include several nucleoside and nucleotide analogs targeting viral DNA polymerase. Although these drugs help manage infections, their common mechanism of action may lead to the development of drug resistance, which is particularly devastating in immunocompromised patients. Therefore, new classes of drugs directed against novel targets in HHVs are necessary to alleviate this issue. We analyzed the conservation rates of all proteins in herpes simplex virus 1 (HHV-1), a representative of the HHV family and one of the most common viruses infecting the human population. Furthermore, we generated a full-length structure model of the most conserved HHV-1 protein, the DNA packaging terminase pUL15. A series of computational analyses were performed on the model to identify ATP and DNA binding sites and characterize the dynamics of the protein. Our study indicates that proteins involved in HHV-1 DNA packaging and cleavage are amongst the most conserved gene products of HHVs. Since the packaging protein pUL15 is the most conserved among all HHV-1 gene products, the virus will have a lower chance of developing resistance to small molecules targeting pUL15. A subsequent analysis of the structure of pUL15 revealed distinct ATP and DNA binding domains and the elastic network model identifies a functionally important hinge region between the two domains of pUL15. The atomic information on the active and allosteric sites in the ATP- and DNA-bound model of pUL15 presented in this study can inform the structure-based drug discovery of a new class of drugs to treat a wide range of HHVs

Grain growth behaviour of an AISI 422 martensitic stainless steel after hot deformation process

The metadynamic softening behaviour and grain size refinement of an AISI 422 martensitic stainless steel in the temperature range of 950–1150°C was investigated by double-hit compression tests. The deformed specimens were held at deformation temperature with delay times of 5–300 s after achieving a strain of 0.3. Based on the experimental results, a model was established for estimation of a softening fraction at different deformation parameters, and the softening fraction was compared with a recrystallised fraction. A major deviation was observed at the beginning of interpass time denoting a significant contribution of recovery to the fractional softening (FS). However, by increasing the time and temperature, the difference between the FS and recrystallised fraction is reduced. The finer grain size was achieved by prior fine pre-austenite grain and lower secondary deformation temperature. The initial grain size of 53 µm decreased down to 32 and 19 µm at the deformation temperatures of 1020 and 940°C, respectively. The austenite grains have considerable growth at a temperature higher than 1020°C, while the grain coarsening is negligible at lower deformation temperatures.Peer ReviewedPostprint (author's final draft

Dynamic recrystallization behavior of AISI 422 stainless steel during hot deformation processes

In this work, hot compression tests were performed to investigate the dynamic recrystallization (DRX) process of a martensitic stainless steel (AISI 422) at temperatures of 950, 1000, 1050, 1100 and 1150 °C and strain rates of 0.01, 0.1 and 1 s−1. The dependency of strain-hardening rate on flow stress was used to estimate the critical stress for the onset of DRX. Accordingly, the critical stress to peak stress ratio was calculated as 0.84. Moreover, the effect of true strain was examined by fitting stress values to an Arrhenius type constitutive equation, and then considering material constants as a function of strain by using a third-order polynomial equation. Finally, two constitutive models were used to investigate the competency of the strain-dependent constitutive equations to predict the flow stress curves of the studied steel. It was concluded that one model offers better precision on the flow stress values after the peak stress, while the other model gives more accurate results before the peak stress.Preprin

On drug-base incompatibilities during extrudate manufacture and fused deposition 3D printing

Aim: 3D printing can be applied for point-of-care personalized treatment. This study aimed to determine the manufacturability and characteristics of 3D printed, drug loaded implants for alcohol misuse. Materials & methods: Disulfiram was the drug substance used and polylactic acid (PLA) the base material. Implantable devices were designed in silico. Drug and PLA were placed into the extruder to produce a 5% blend at 1.75-mm diameter. Material characterization included differential scanning calorimetry, thermogravimetric analysis plus inverse GC-surface energy analyzer. Results: Implantable constructs from the PLA feedstock were acquired. The extrusion processes had a detrimental effect on the active pharmaceutical ingredient-base blend. differential scanning calorimetry and thermogravimetric analysis analysis indicated drug–base interactions. Thermal history was found to influence inverse GC probe interaction. Conclusion: Drug-base incompatibilities must be considered during 3D printing

The Progress and Pitfalls of Pharmacogenetics-Based Precision Medicine in Schizophrenia Spectrum Disorders:A Systematic Review and Meta-Analysis

The inadequate efficacy and adverse effects of antipsychotics severely affect the recovery of patients with schizophrenia spectrum disorders (SSD). We report the evidence for associations between pharmacogenetic (PGx) variants and antipsychotics outcomes, including antipsychotic response, antipsychotic-induced weight/BMI gain, metabolic syndrome, antipsychotic-related prolactin levels, antipsychotic-induced tardive dyskinesia (TD), clozapine-induced agranulocytosis (CLA), and drug concentration level (pharmacokinetics) in SSD patients. Through an in-depth systematic search in 2010–2022, we identified 501 records. We included 29 meta-analyses constituting pooled data from 298 original studies over 69 PGx variants across 39 genes, 4 metabolizing phenotypes of CYP2D9, and 3 of CYP2C19. We observed weak unadjusted nominal significant (p &lt; 0.05) additive effects of PGx variants of DRD1, DRD2, DRD3, HTR1A, HTR2A, HTR3A, and COMT (10 variants) on antipsychotic response; DRD2, HTR2C, BDNF, ADRA2A, ADRB3, GNB3, INSIG2, LEP, MC4R, and SNAP25 (14 variants) on weight gain; HTR2C (one variant) on metabolic syndrome; DRD2 (one variant) on prolactin levels; COMT and BDNF (two variants) on TD; HLA-DRB1 (one variant) on CLA; CYP2D6 (four phenotypes) and CYP2C19 (two phenotypes) on antipsychotics plasma levels. In the future, well-designed longitudinal naturalistic multi-center PGx studies are needed to validate the effectiveness of PGx variants in antipsychotic outcomes before establishing any reproducible PGx passport in clinical practice.</p

The effect of atrovastatin on the ovarian arterial blood flow and serum androgen level in PCOS patient

Various researches have been conducted over the recent years on the therapeutic effects of statins on the metabolic and hyper-androgenic state of the patients suffering from PCOS. The present research seeks to evaluate the treatment with atorvastatin and its effect on the lipid profile level, serum androgen status and morphology and blood flow of polycystic ovaries. A double blind clinical trial was designed for this research where the women with PCOS resorting to the gynecology clinic of Firouzgar Hospital were randomly divided into two groups: case and Control. Early at the beginning of the research, variables such as body mass, lipid profile, blood androgen level, fasting blood Sugar, size of the ovary, and resistance of the stromal artery of ovary were studied. For a period of 6 weeks, one group was given with a daily dose of 40 mg atorvastatin, while the other group just received placebo. All the variables were studied once again after 6 weeks and the results were analyzed using SPSS v.16. The case group included 20 patients suffering from PCOS who received atorvastatin, while there were 20 patients with PCOS in the witness group who just received placebo. The average ages in the atorvastatin and placebo groups were 27.7 ± 3.41 and 30.9 ± 4.8 years old respectively. A significant difference was observed between the two groups in terms of changes in the average cholesterol and LDL levels before and after the intervention. This reduction was more significant in the atorvastatin group. After prescription of atorvastatin, the level of Androstenedione had decreased significantly in treatment group. A statistically significant reduction was observed in the size of left and right ovaries in the group receiving atorvastatin. No significant changes were observed in the size of the ovaries in the group receiving placebo. The average arterial resistance level of left and right ovaries before and after intervention in atorvastatin group exhibited a significant reduction. Having discarded the confounding effect of RI, this difference with the witness group was statistically significant. Keeping in mind the effects of atorvastatin such as improving the lipid profile status and reduction of androstenedione among those with PCOS, it can be used as an auxiliary treatment to control symptoms and long-term side effects among patients. Considering the shrinkage of ovary size and enhancement of blood flow to PCOS ovary, future researches can focus on effectiveness of statins in improving the ovulation status of performance of PCO ovaries