Predicting the number of IT staff needed in hospitals of Isfahan University of Medical Sciences based on modeling in 2023: A descriptive-analytical study.

Background and Aims: Considering the increasing use of information technology (IT) and the need of the implementation of related projects, the lack of IT specialists in the health system is one of the major challenges that require planning and foreseeing. This study was conducted with the aim of predicting the number of required IT personnel in hospitals of Isfahan University of Medical Sciences based on the modeling of identified and weighed influential factors in 2023. Method: First, Delphi method and multi-criteria decision-making (MCDM) using the Expository Posthaste Effective Resemblant Tool (ExPERT) were conducted to identify and weigh the components that affect IT staff's workload in hospitals. Then, the model for predicting the required number of IT personnel for the involved hospitals was developed. In all stages, the obtained information and results were checked and confirmed using experts' opinions in Focus Group Discussions. Results: Twenty-one hospitals (57%) out of 37 hospitals are facing a shortage of IT personnel. This varies from 0.5 to 1.6 personnel in different hospitals. Thirteen hospitals (35%) were reported to have adequate IT staffing and three hospitals (8%) had excess IT staffing. Conclusion: This study provided a predictive model for required IT staff in hospitals using MCDM through ExPERT which can be used in cases where the use of workload-based methods such as Workload Indicators of Staffing Need is complex or time-consuming.

An ensemble-based approach to estimate confidence of predicted protein-ligand binding affinity values.

When designing a machine learning-based scoring function, we access a limited number of protein-ligand complexes with experimentally determined binding affinity values, representing only a fraction of all possible protein-ligand complexes. Consequently, it is crucial to report a measure of confidence and quantify the uncertainty in the model's predictions during test time. Here, we adopt the conformal prediction technique to evaluate the confidence of a prediction for each member of the core set of the CASF 2016 benchmark. The conformal prediction technique requires a diverse ensemble of predictors for uncertainty estimation. To this end, we introduce ENS-Score as an ensemble predictor, which includes 30 models with different protein-ligand representation approaches and achieves Pearson's correlation of 0.842 on the core set of the CASF 2016 benchmark. Also, we comprehensively investigate the residual error of each data point to assess the normality behavior of the distribution of the residual errors and their correlation to the structural features of the ligands, such as hydrophobic interactions and halogen bonding. In the end, we provide a local host web application to facilitate the usage of ENS-Score. All codes to repeat results are provided at https://github.com/miladrayka/ENS_Score.

Virtual Source Synthetic Aperture for Accurate Lateral Displacement Estimation in Ultrasound Elastography.

Ultrasound elastography (USE) is an emerging noninvasive imaging technique in which pathological alterations can be visualized by revealing the mechanical properties of the tissue. Estimating tissue displacement in all directions is required to accurately estimate the mechanical properties. Despite capabilities of elastography techniques in estimating displacement in both axial and lateral directions, estimation of axial displacement is more accurate than lateral direction due to higher sampling frequency, higher resolution, and having a carrier signal propagating in the axial direction. Among different ultrasound imaging techniques, synthetic aperture (SA) has better lateral resolution than others, but it is not commonly used for USE due to its limitation in imaging depth of field. Virtual source synthetic aperture (VSSA) imaging is a technique to implement SA beamforming on the focused transmitted data to overcome the limitation of SA in depth of field while maintaining the same lateral resolution as SA. Besides lateral resolution, VSSA has the capability of increasing sampling frequency in the lateral direction without interpolation. In this article, we utilize VSSA to perform beamforming to enable higher resolution and sampling frequency in the lateral direction. The beamformed data are then processed using our recently published elastography technique, OVERWIND. Simulation and experimental results show substantial improvement in the estimation of lateral displacements.

Synthetic aperture with high lateral sampling frequency for ultrasound elastography.

Ultrasound elastography is a non-invasive technique for detecting pathological alterations in tissue. It is known that pathological alteration of tissue often has a direct impact on its elastic modulus, which can be revealed using elastography. For estimating elastic modulus, we need to estimate both axial and lateral displacement accurately. Current state of the art elastography techniques provide a substantially less accurate lateral displacement field as compared to the axial displacement field. One of the most important factors in poor lateral estimation is a low sampling frequency in the lateral direction. In this paper, we use synthetic aperture beamforming to benefit from its capability of high sampling frequency in the lateral direction. We compare highly sampled data and focused line per line beam formed data by feeding them to our recently published elastography method, OVERWIND [1]. According to simulation and phantom experiments, not only the lateral displacement estimation is substantially improved, but also the axial displacement estimation is improved.

Accurate and Precise Time-Delay Estimation for Ultrasound Elastography With Prebeamformed Channel Data.

Free-hand palpation ultrasound elastography is a noninvasive approach for detecting pathological alteration in tissue. In this method, the tissue is compressed by a handheld probe and displacement of each sample is estimated, a process which is also known as time-delay estimation (TDE). Even with the simplifying assumption that ignores out of plane motion, TDE is an ill-posed problem requiring estimation of axial and lateral displacements for each sample from its intensity. A well-known class of methods for making elastography a well-posed problem is regularized optimization-based methods, which imposes smoothness regularization in the associated cost function. In this article, we propose to utilize channel data that have been compensated for time gain and time delay (introduced by transmission) instead of postbeamformed radio frequency (RF) data in the optimization problem. We name our proposed method Channel data for GLobal Ultrasound Elastography (CGLUE). We analytically derive bias and variances of TDE as functions of data noise for CGLUE and Global Ultrasound Elastography (GLUE) and use the Cauchy-Schwarz inequality to prove that CGLUE provides a TDE with lower bias and variance error. To further illustrate the improved performance of CGLUE, the results of simulation, experimental phantom, and ex-vivo experiments are presented.

3D normalized cross-correlation for estimation of the displacement field in ultrasound elastography.

This paper introduces a novel technique to estimate tissue displacement in quasi-static elastography. A major challenge in elastography is estimation of displacement (also referred to time-delay estimation) between pre-compressed and post-compressed ultrasound data. Maximizing normalized cross correlation (NCC) of ultrasound radio-frequency (RF) data of the pre- and post-compressed images is a popular technique for strain estimation due to its simplicity and computational efficiency. Several papers have been published to increase the accuracy and quality of displacement estimation based on NCC. All of these methods use 2D spatial windows in RF data to estimate NCC, wherein displacement is assumed to be constant within each window. In this work, we extend this assumption along the third dimension. Two approaches are proposed to get third dimension. In the first approach, we use temporal domain to exploit neighboring samples in both spatial and temporal directions. Considering temporal information is important since traditional and ultrafast ultrasound machines are, respectively, capable of imaging at more than 30 frame per second (fps) and 1000 fps. Another approach is to use time-delayed pre-beam formed data (channel data) instead of RF data. In this method information of all channels that are recorded as pre-beam formed data of each RF line will be considered as 3rd dimension. We call these methods as spatial temporal normalized cross correlation (STNCC) and channel data normalized cross correlation (CNCC) and show that they substantially outperforms NCC using simulation, phantom and in-vivo experiments. Given substantial improvements of results in addition to the relative simplicity of implementing STNCC and CNCC, the proposed approaches can potentially have a large impact in both academic and commercial work on ultrasound elastography.

Combining Total Variation Regularization with Window-Based Time Delay Estimation in Ultrasound Elastography.

A major challenge of free-hand palpation ultrasound elastography (USE) is estimating the displacement of RF samples between pre- and post-compressed RF data. The problem of displacement estimation is ill-posed since the displacement of one sample by itself cannot be uniquely calculated. To resolve this problem, two categories of methods have emerged. The first category assumes that the displacement of samples within a small window surrounding the reference sample is constant. The second class imposes smoothness regularization and optimizes an energy function. Herein, we propose a novel method that combines both approaches, and as such, is more robust to noise. The second contribution of this work is the introduction of the L1 norm as the regularization term in our cost function, which is often referred to as the total variation (TV) regularization. Compared to previous work that used the L2 norm regularization, optimization of the new cost function is more challenging. However, the advantages of using the L1 norm are twofold. First, it leads to substantial improvement in the sharpness of displacement estimates. Second, to optimize the cost function with the L1 norm regularization, we use an iterative method that further increases the robustness. We name our proposed method tOtal Variation Regularization and WINDow-based time delay estimation (OVERWIND) and show that it is robust to signal decorrelation and generates sharp displacement and strain maps for simulated, experimental phantom and in-vivo data. In particular, OVERWIND improves strain contrast-to-noise ratio (CNR) by 27.26%, 144.05%, and 49.90% on average in simulation, phantom, and in-vivo data, respectively, compared to our recent Global Ultrasound Elastography (GLUE) method.

An ice nucleation protein from Fusarium acuminatum: cloning, expression, biochemical characterization and computational modeling.

Ice nucleation proteins (INP) are a major cause of frost damage in plants and crops. Here, an INP gene from Fusarium acuminatum was optimized, synthesized, expressed in E.coli and subsequently purified and characterized. The protein belongs to the second class of ice nucleation proteins with an optimum pH 5.5, relative activity and stability between pH 5 and 9.5 and up to 45 °C. The protein was fully active and stable in the presence of dimethyl sulfoxide (DMSO), dioxane, acetone and ethyl acetate. Moreover, it retained over 50 % of its original activity in the presence of polyvinyl alcohol. The 3D structure model of the INP-F indicated the protein had three distinct domains as exist in other ice nucleation proteins with some variations. Considering these promising results, INP-F could be a novel candidate for industrial applications.

Antioxidant activity of different parts of Tetrataenium lasiopetalum.

CONTEXT: In Iranian traditional medicine, different species of the genus Tetrataenium are used as antiseptic, spice and food additives. OBJECTIVE: The present study examined the possible antioxidant effects of hydro-alcoholic extracts of different parts of Tetrataenium lasiopetalum (Boiss.) Manden (Apiaceae). MATERIALS AND METHODS: Laminas, stems, petioles, fruits, peduncles and flowers of T. lasiopetalum were collected, dried and then extracted by ethanol and water (70:30). Antioxidant activities of extracts were examined by employing different in vitro assays, i.e., 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging, metal chelating, reducing power activities and hemoglobin-induced linoleic acid system. Also, total phenolic and flavonoid contents of the extracts were evaluated. RESULTS: Hydro-alcoholic extract of T. lasiopetalum flower showed the highest activity in scavenging of DPPH (IC50 = 170 ± 7 µg/mL). In metal chelating assay, lamina extract possesses a better iron ion chelating activity than other extracts (230 ± 10 µg/mL). Lamina hydro-alcoholic extract demonstrated better activity in reducing the power and hemoglobin-induced linoleic acid system than other parts of T. lasiopetalum. DISCUSSION AND CONCLUSION: These results showed the antioxidant activity of different parts of T. lasiopetalum based on its usage in traditional medicine.

Purification and autolysis of the ficin isoforms from fig (Ficus carica cv. Sabz) latex.

Ficin (EC 3.4.22.3), a cysteine endoproteolytic protease in fig trees' latex, has multiple isoforms. Until now, no data on autolysis of individual ficins (ficin isoforms) are available. Following purification, ficins' autolysis was determined by HPLC chromatogram changes and ultrafiltrations at different temperatures and storage times. These results showed that the number of HPLC peaks in latex proteins purification of Ficus carica cv. Sabz varied from previous fig varieties or cultivars. Proteolytic activity of ficins was inhibited by specific cysteine protease inhibitors, confirming the participation of the cysteine residue in the active site. The zeta potential of the first two eluted peaks (I and II) was negative, while that of other peaks were positive. All ficins were susceptible to autolysis when stored at high temperatures. In contrast, only the last two ficins (B, C) were prone to autolysis at cold temperature after long storage period. The rate of degradation of the ficins was significantly increased with the increased storage time. The ficin (A) related to peak (III) had the highest and the lowest surface hydrophobic patches and ratio of autolytic to proteolytic activity, respectively.

Neuroprotective effects of methyl-3-O-methyl gallate against sodium fluoride-induced oxidative stress in the brain of rats.

Methyl-3-O-methyl gallate (M3OMG) is a rare natural product that showed promising in vitro antioxidant activities. In this study, the protective role of synthetic M3OMG against sodium fluoride (NaF)-induced oxidative stress in rat brain was evaluated. Animals were treated with either M3OMG (10 and 20 mg/kg i.p.), vitamin C (10 mg/kg i.p.) as the standard antioxidant or the vehicle (5 % dimethyl sulfoxide; 1 ml/kg) for 1 week. Oxidative stress was induced in the brain by adding 600 ppm NaF in the drinking water for 7 days. At the end of the treatment period, the levels of thiobarbituric acid reactive substances (TBARS), reduced glutathione and the activities of antioxidant enzymes (superoxide dismutase and catalase) were evaluated in brain homogenates. M3OMG treatment mitigated the NaF-induced oxidative stress through normalization of the level of TBARS, reduced levels of glutathione and by the restoration of the diminished antioxidant enzyme activities. In conclusion, M3OMG could have a potential for treating neurotoxicity induced by fluoride or related environmental pollutants.

Effect of silymarin on sodium fluoride-induced toxicity and oxidative stress in rat cardiac tissues.

This study aim to evaluate the protective effect of silymarin on sodium fluoride-induced oxidative stress in rat cardiac tissues. Animals were pretreated with silymarin at 20 and 10 mg/kg prior to sodium fluoride consumption (600 ppm through drinking water). Vitamin C at 10 mg/kg was used as standard antioxidant. There was a significant increase in thiobarbituric acid reactive substances level (59.36 ± 2.19 nmol MDA eq/g tissue) along with a decrease in antioxidant enzymes activity (64.27 ± 1.98 U/g tissue for superoxide dismutase activity and 29.17 ± 1.01 µmol/min/mg protein for catalase activity) and reduced glutathione level (3.8 ± 0.15 µg/mg protein) in the tissues homogenates of the sodium fluoride-intoxicated rats. Silymarin administration to animals before sodium fluoride consumption modified the levels of biochemical parameters.

Mitigating role of quercetin against sodium fluoride-induced oxidative stress in the rat brain.

CONTEXT: Quercetin is a well known aglycone flavonoid that is widely found in different food sources. OBJECTIVE: In this study, the in vivo neuroprotective potential of quercetin against sodium fluoride-induced oxidative stress was evaluated. MATERIALS AND METHODS: Wistar rats were divided into five treatment groups and then subjected to daily intraperitoneally treatment with quercetin (at 10 and 20 mg/kg body weight), vitamin C (at 10 mg/kg), or vehicle. After a 1 week treatment period, all groups except saline treated (normal group), were intoxicated with sodium fluoride (NaF) for 1 week. Rat brains were then removed and homogenized for measurement of antioxidant markers including superoxide dismutase (SOD), reduced glutathione, catalase, and lipid peroxidation final products. RESULTS: The thiobarbituric acid reactive substances (TBARS) levels in the heart homogenate of sodium fluoride treated rats (42.04 ± 2.14 nmol MDA eq/g tissue) increased compared to the normal rats (35.99 ± 1.08 nmol MDA eq/g tissue). Animals which were pretreated with quercetin at 20 mg/kg for 1 week prior to sodium fluoride intoxication showed significant reduction in the TBARS level (36.13 ± 1.12 nmol MDA eq/g tissue). Also, pretreatment with quercetin (20 mg/kg) restored the SOD and catalase activities and modified the level of reduced glutathione compared with the control group (p > 0.05). DISCUSSION AND CONCLUSION: The present study revealed a potent neuroprotective potential of quercetin against NaF-induced toxicity.

Surface display of organophosphorus hydrolase on E. coli using N-terminal domain of ice nucleation protein InaV.

Recombinant Escherichia coli displaying organophosphorus hydrolase (OPH) was used to overcome the diffusion barrier limitation of organophosphorus pesticides. A new anchor system derived from the N-terminal domain of ice-nucleation protein from Pseudomonas syringae InaV (InaV-N) was used to display OPH onto the surface. The designed sequence was cloned in the vector pET-28a(+) and then was expressed in E. coli. Tracing of the expression location of the recombinant protein using SDS-PAGE showed the presentation of OPH by InaV-N on the outer membrane, and the ability of recombinant E. coli to utilize diazinon as the sole source of energy, without growth inhibition, indicated its significant activity. The location of OPH was detected by comparing the activity of the outer membrane fraction with the inner membrane and cytoplasm fractions. Studies revealed that recombinant E. coli can degrade 50% of 2 mM chlorpyrifos in 2 min. It can be concluded that InaV-N can be used efficiently to display foreign functional protein, and these results highlight the high potential of an engineered bacterium to be used in bioremediation of pesticide-contaminated sources in the environment.

Protective effect of quercetin against sodium fluoride induced oxidative stress in rat's heart.

The antioxidative and cardioprotective properties of quercetin were investigated against sodium fluoride (NaF) induced oxidative stress in rat hearts. Experimental rats were divided into five groups. The first group served as the untreated (normal) control. The second group received NaF at a dose of 600 ppm through drinking water for 1 week, and served as the toxin control. The third and fourth groups were exposed to quercetin (at the dose of 10 and 20 mg kg(-1) intraperitoneally (i.p.) for 1 week) prior to NaF intoxication, and the fifth group was treated with vitamin C at a dose of 10 mg kg(-1) i.p., for 1 week prior to NaF intoxication and served as the positive control in the study. The activities of various antioxidant enzymes, superoxide dismutase and catalase, level of reduced glutathione and lipid peroxidation end product were determined in the cardiac tissues of all the experimental animals. NaF intoxication significantly altered all the indices related to the pro-oxidant-antioxidant status of the heart; treatment with the active constituents prior to NaF administration, however, prevented these alterations. The combined results suggest that quercetin protects rat hearts from NaF-induced oxidative stress, probably via its antioxidant properties.