Likelihood-based estimation of substructure content from single-wavelength anomalous diffraction (SAD) intensity data.

SAD phasing can be challenging when the signal-to-noise ratio is low. In such cases, having an accurate estimate of the substructure content can determine whether or not the substructure of anomalous scatterer positions can successfully be determined. Here, a likelihood-based target function is proposed to accurately estimate the strength of the anomalous scattering contribution directly from the measured intensities, determining a complex correlation parameter relating the Bijvoet mates as a function of resolution. This gives a novel measure of the intrinsic anomalous signal. The SAD likelihood target function also accounts for correlated errors in the measurement of intensities from Bijvoet mates, which can arise from the effects of radiation damage. When the anomalous signal is assumed to come primarily from a substructure comprising one anomalous scatterer with a known value of f'' and when the protein composition of the crystal is estimated correctly, the refined complex correlation parameters can be interpreted in terms of the atomic content of the primary anomalous scatterer before the substructure is known. The maximum-likelihood estimation of substructure content was tested on a curated database of 357 SAD cases with useful anomalous signal. The prior estimates of substructure content are highly correlated to the content determined by phasing calculations, with a correlation coefficient (on a log-log basis) of 0.72

Work-related stress dimensions among a subsidiary company workers of Iranian oil refining and distribution company

Introduction Work-related stress and its causes are among the most important issues which can seriously challenge organizational efficiency and employees' health. Different occupational environments and groups have different levels of job stress. The present study aimed to investigate relationships between job stress and its dimensions with three occupational groups (administrative, administrative-operational, and operational) among a subsidiary company workers of Iranian Oil Refining and Distribution Company. Methods The present study had descriptive-analytical and cross-sectional type and was conducted among 468 out of 503 employees (with entry condition of a year of work experience as well as an official and contractual membership) volunteered to participate in research. Data collection tools included demographic questions and job stress questionnaire as well as human resource department information to determine occupational group of employees. Descriptive statistics, statistical tests, Independent test, and one-way ANOVA in addition to SPSS 21 software were used for data analysis. Results There were significant relationships between age, education levels, work experience and smoking with mean score of job stress (P-value 0.05). Conclusions Exposure to different occupational harmful agents, facing with different safety risks, being far from family, heavy workload, and uncertain employee roles have significantly increased job stress in both operational and executive occupation groups compared to other two occupational groups; hence, there is a positive correlation between high job stress and operational jobs

Demographic and clinicopathologic profile of malignant epithelial ovarian tumors: an experience from a tertiary cancer care centre in Bangalore, South India

Background: Ovarian cancer is fast emerging as the leading cancer of the female genital tract. It is the second most common gynecological malignancy in India, but has poor outcomes making it the leading cause of gynecologic cancer related deaths. There is a paucity of data regarding demographic details, patterns of care and outcomes of ovarian epithelial malignancies in India. This is a study to evaluate the demographic details, clinical profile and pathology details of epithelial ovarian cancer registering in atertiary cancer center in Bangalore, Karnataka, India.Methods: This is a retrospective study of the case records of patients diagnosed with epithelial ovarian cancer from January 2012 to December 2014.Results: Malignantovarian tumors constituted 5.6% of all malignancies in women. 84 cases were of epithelial origin constituting 64.4% of all malignant ovarian tumors. 58% of patients were from Karnataka and 25% were from West Bengal. 27% underwent suboptimal surgery outside at presentation. The median age at presentation was 51 years. Most of the patients were parous (25% were para 2 and 3). 5% patients were nulliparous. Pain abdomen (39%) and abdominal distension/ bloating (16%) were the most common symptoms. 75% of these cases presented in III-IV stage. Method of diagnosis was: primary surgery and Biopsy of mass (50%), fine needle aspiration cytology of mass or ascites/ pleural effusion (40%), and diagnostic laparoscopy in (9.5%) of the patients. The most common histological variants were serous cystadenocarcinoma (32%) and mucinous adenocarcinoma (15%).Conclusions: Majority of the patients presented with vague nonspecific abdominal complaints which leads to delay in diagnosis. Most of the patients presented in advanced stage of the disease. Delay in diagnosis and improper management prior to registering in tertiary cancer centre was common. There is a need to improve awareness regarding ovarian cancer in general population and also primary care physician

Factors influencing estimates of coordinate error for molecular replacement.

Good prior estimates of the effective root-mean-square deviation (r.m.s.d.) between the atomic coordinates of the model and the target optimize the signal in molecular replacement, thereby increasing the success rate in difficult cases. Previous studies using protein structures solved by X-ray crystallography as models showed that optimal error estimates (refined after structure solution) were correlated with the sequence identity between the model and target, and with the number of residues in the model. Here, this work has been extended to find additional correlations between parameters of the model and the target and hence improved prior estimates of the coordinate error. Using a graph database, a curated set of 6030 molecular-replacement calculations using models that had been solved by X-ray crystallography was analysed to consider about 120 model and target parameters. Improved estimates were achieved by replacing the sequence identity with the Gonnet score for sequence similarity, as well as by considering the resolution of the target structure and the MolProbity score of the model. This approach was extended by analysing 12 610 additional molecular-replacement calculations where the model was determined by NMR. The median r.m.s.d. between pairs of models in an ensemble was found to be correlated with the estimated r.m.s.d. to the target. For models solved by NMR, the overall coordinate error estimates were larger than for structures determined by X-ray crystallography, and were more highly correlated with the number of residues

Likelihood‐based estimation of substructure content from single‐wavelength anomalous diffraction (SAD) intensity data

SAD phasing can be challenging when the signal‐to‐noise ratio is low. In such cases, having an accurate estimate of the substructure content can determine whether or not the substructure of anomalous scatterer positions can successfully be determined. Here, a likelihood‐based target function is proposed to accurately estimate the strength of the anomalous scattering contribution directly from the measured intensities, determining a complex correlation parameter relating the Bijvoet mates as a function of resolution. This gives a novel measure of the intrinsic anomalous signal. The SAD likelihood target function also accounts for correlated errors in the measurement of intensities from Bijvoet mates, which can arise from the effects of radiation damage. When the anomalous signal is assumed to come primarily from a substructure comprising one anomalous scatterer with a known value of f′′ and when the protein composition of the crystal is estimated correctly, the refined complex correlation parameters can be interpreted in terms of the atomic content of the primary anomalous scatterer before the substructure is known. The maximum‐likelihood estimation of substructure content was tested on a curated database of 357 SAD cases with useful anomalous signal. The prior estimates of substructure content are highly correlated to the content determined by phasing calculations, with a correlation coefficient (on a log–log basis) of 0.72

commerciallyClinical study of rhino-orbital-cerebral mucormycosis in COVID-19 patients in a regional institute in South India

BACKGROUND: Rhino-orbital-cerebral mucormycosis (ROCM) is usually seen in immunosuppressed conditions like uncontrolled diabetes mellitus (DM). The pandemic of severe acute respiratory syndrome coronavirus 2 (Sars-CoV-2) and its associated immunosuppression and indiscriminate use of corticosteroids emerged as a new risk factor for ROCM during its’ second wave of coronavirus disease 2019 (COVID-19), especially in India. The lack of standardized management protocol for ROCM needs the attention of the ophthalmic community. COVID-19-associated risk factors have been linked to the pathogenesis of ROCM, which reached epidemic proportions during India’s second wave of the pandemic. The aim of the present study was to document cases of ROCM and to evaluate risk factors, including co-morbidities, clinical characteristics, diagnosis, management, and outcome at tertiary care centers during the Sars-CoV-2 (2021) pandemic. MATERIAL AND METHODS: It is a retrospective study of 42 patients of biopsy-proven mucormycosis. These patients’ records were reviewed from hospital data. All patients were subjected to complete ophthalmological, ortorhino laringological examination, and imaging studies. The orbital staging was done. Each case was treated by a multidisciplinary approach with functional endoscopic sinus surgery (FESS) and intravenous (i.v.) amphotericin B (AMB). Retrobulbar liposomal AMB and exenteration were performed whenever indicated. Statistical analysis was done using the Chi square test. A p-value ≤ 0.05 was considered significant. RESULTS: Total 42 patients of ROCM were documented. The mean age was 50.48 years, with a male preponderance (82.9%). 99.8% of patients had diabetes (39 patients) and all patients were COVID-19-positive. Concurrent steroid use was seen in 83.3% where 73.1% of patients had received oxygen support during COVID-19 infection. The most common ophthalmologic presentation was orbital/facial oedema (33) and pain, diminution of vision (24), and ophthalmoplegia (26). Direct nasal endoscopy and biopsy were done to establish a diagnosis. All patients were treated with FESS and i.v. AMB. Retrobulbar AMB was given to 11 patients. Exenteration was done in (n = 4) 10.5% of cases. 41 patients recovered, and one patient died CONCLUSION: The most significant predisposing factors for developing COVID-19-associated ROCM are corticosteroids and DM. Patients with COVID-19 must be followed up even after recovery. For a favorable outcome with lower mortality in COVID-19 recovered patients, we must have a high index of clinical suspicion with awareness of red flag signs and make a timely diagnosis

The effect of salts on the liquid–liquid phase equilibria of PEG600 + salt aqueous two-phase systems

Six new ATPSs were prepared by combining polyethylene glycol PEG600 with potassium citrate, dipotassium hydrogen phosphate, sodium formate, potassium formate, sodium sulfate, and lithium sulfate. Complete phase diagrams, including the binodal curve and three tie-lines, were determined at 23 °C. The experimental data obtained for the binodal curve were successfully adjusted to the Merchuk equation, and the reliability of tie-line data was confirmed using the equations suggested by Othmer–Tobias and Bancroft. The ability of each ion to induce ATPS formation was investigated. Na+ proved to be more effective in ATPS formation than K+ and Li+. For potassium salts, the order observed for the effectiveness of the anions was: HPO42– > C6H5O73– > HCO2–. Regarding the sodium salts, it was found that SO42– is clearly more effective than HCO2–. The position of the ions in the Hofmeister series and their free energy of hydration (ΔGhyd) were used to explain the ability of the ions to induce PEG salting-out. Furthermore, the effective excluded volume (EEV) of the salts was determined and the following order was found: Na2SO4 > K2HPO4 > Li2SO4 > K3C6H5O7 > NaCHO2 > KCHO2. Similar order was obtained when analyzing the size of the heterogeneous regions, suggesting the practical use of EEV as a comparison parameter between different ATPSs.This work is partially supported by project PEst-C/EQB/LA0020/2011, financed by FEDER through COMPETE-Programa Operacional Factores de Competitividade and by FCT-Fundacao para a Ciencia e a Tecnologia. Sara Silverio acknowledges her Ph.D. grant from FCT (SFRH/BD/43439/2008)