Blocking the dopaminergic receptors within the hippocampal dentate gyrus reduced analgesic responses induced by restraint stress in the formalin test

Previous studies have shown that various receptors, including dopamine receptors, are expressed in the hippocampal dentate gyrus (DG). Besides, indicatively, dopamine receptors play an essential role in the modulation of pain perception. On the other hand, stressful experiences can produce analgesia, termed stress-induced analgesia (SIA). The current study examined the probable role of dopamine receptors within the DG in antinociception induced by restraint stress (RS). Ninety-seven male albino Wistar rats were unilaterally implanted with a cannula in the DG. Animals received intra-DG microinjections of SCH23390 or Sulpiride (0.25, 1, and 4 μg/rat) as D1-and D2-like dopamine receptor antagonists, respectively, five minutes before RS. Ten minutes after the end of the induction of RS for three hours, 50 μl 2.5% formalin was injected subcutaneously into the plantar surface of the hind paw to induce persistent inflammatory pain. Pain scores were evaluated at 5-minute intervals for 60 minutes. These findings showed that; exposure to RS for three hours produced SIA in both phases of the formalin test, while this RS-induced analgesia was attenuated in the early and late phases of the formalin test by intra-DG microinjection of SCH23390 and Sulpiride. The results of the present study suggested that both D1- and D2-like dopamine receptors in the DG have a considerable role in the induced analgesia by RS.

Contribution of the intra-hippocampal orexin system in the regulation of restraint stress response to pain-related behaviors in the formalin test

Stress-induced antinociception (SIA) is due to the activation of several neural pathways and neurotransmitters that often suppress pain perception. Studies have shown that the orexin neuropeptide system is essential in pain modulation. Therefore, this study aimed to investigate the role of orexinergic receptors in the hippocampal CA1 region in modulating SIA response during the formalin test as an animal model of inflammatory pain. The orexin-1 receptor (OX1r) antagonist, SB334867, at 1, 3, 10, and 30 nmol or TCS OX2 29 as an orexin-2 receptor (OX2r) antagonist at the same doses were microinjected into the CA1 region in rats. Five minutes later, rats were exposed to restraint stress (RS) for 3 h, and pain-related behaviors were monitored in 5-min blocks for the 60-min test period in the formalin test. Results showed that applying RS for 3 h reduced pain responses in the early and late phases of the formalin test. The main findings showed that intra-CA1 injection of orexin receptor antagonists reduced the antinociception caused by stress in both phases of the formalin test. In addition, the contribution of OX2r in mediating the antinociceptive effect of stress was more prominent than that of OX1r in the early phase of the formalin test. However, in the late phase, both receptors worked similarly. Accordingly, the orexin system and its two receptors in the CA1 region of the hippocampus regulate SIA response to this animal model of pain in formalin test.

Single-cell multi-omics analysis identifies context-specific gene regulatory gates and mechanisms

There is a growing interest in inferring context specific gene regulatory networks from single-cell RNA sequencing (scRNA-seq) data. This involves identifying the regulatory relationships between transcription factors (TFs) and genes in individual cells, and then characterizing these relationships at the level of specific cell types or cell states. In this study, we introduce scGATE (single-cell gene regulatory gate) as a novel computational tool for inferring TF-gene interaction networks and reconstructing Boolean logic gates involving regulatory TFs using scRNA-seq data. In contrast to current Boolean models, scGATE eliminates the need for individual formulations and likelihood calculations for each Boolean rule (e.g. AND, OR, XOR). By employing a Bayesian framework, scGATE infers the Boolean rule after fitting the model to the data, resulting in significant reductions in time-complexities for logic-based studies. We have applied assay for transposase-accessible chromatin with sequencing (scATAC-seq) data and TF DNA binding motifs to filter out non-relevant TFs in gene regulations. By integrating single-cell clustering with these external cues, scGATE is able to infer context specific networks. The performance of scGATE is evaluated using synthetic and real single-cell multi-omics data from mouse tissues and human blood, demonstrating its superiority over existing tools for reconstructing TF-gene networks. Additionally, scGATE provides a flexible framework for understanding the complex combinatorial and cooperative relationships among TFs regulating target genes by inferring Boolean logic gates among them.

A comparative study on the effect of limestone particle size on performance, ileal digestibility of calcium and phosphorus, and bone characteristics in broilers and pullets

1. The effects of limestone particle size on growth performance, gastrointestinal tract (GIT) traits, ileal morphology, duodenal gene expression of calbindin, apparent ileal digestibility coefficients (AIDC) of calcium (Ca) and phosphorus (P) and tibia characteristics in broilers and pullets were assessed in broilers and pullets. These birds have different growth rates and likely different responses to parameters, such as particle size.2. A total of 240 chicks aged one day, 120 Ross 308 female broilers, and 120 Hy-Line pullets were allocated randomly into four treatments in a 2 × 2 factorial arrangement with two bird types (broilers vs. pullets) and two limestone particle sizes (<0.5 mm versus 1-2 mm) to give six replicates containing 10 chicks in each from 1 to 21 d of age.3. Feed intake and weight gain were greater (P < 0.001) and feed per gain (FCR) was better (P < 0.001) in broilers compared to pullets from 1 to 21 d of age. Greater villus width (P < 0.01), villus height (P < 0.001) and crypt depth (P < 0.01) were seen for broilers compared to pullets.4. Pullets fed coarse Ca particles had higher calbindin gene expression at 21 d of age (P = 0.05). Both AIDC of Ca and P were higher (P < 0.001) in broilers compared to pullets. The AIDC of Ca from 0.463 to 0.516 was increased (P < 0.05) by feeding coarse limestone particles. A significant interaction was found between bird type and limestone particle size (P < 0.01), where pullets fed coarse Ca particles had higher bone P concentration in tibia than broilers.5. Broilers had better ileum absorptive capacity and growth performance compared to pullets. The AIDC of Ca and P was higher in broilers than in pullets. Increased limestone particle size elevated villus height, AIDC of Ca and concentration of P in the tibia.

A computational model of stem cells' internal mechanism to recapitulate spatial patterning and maintain the self-organized pattern in the homeostasis state

The complex functioning of multi-cellular tissue development relies on proper cell production rates to replace dead or differentiated specialized cells. Stem cells are critical for tissue development and maintenance, as they produce specialized cells to meet the tissues' demands. In this study, we propose a computational model to investigate the stem cell's mechanism, which generates the appropriate proportion of specialized cells, and distributes them to their correct position to form and maintain the organized structure in the population through intercellular reactions. Our computational model focuses on early development, where the populations overall behavior is determined by stem cells and signaling molecules. The model does not include complicated factors such as movement of specialized cells or outside signaling sources. The results indicate that in our model, the stem cells can organize the population into a desired spatial pattern, which demonstrates their ability to self-organize as long as the corresponding leading signal is present. We also investigate the impact of stochasticity, which provides desired non-genetic diversity; however, it can also break the proper boundaries of the desired spatial pattern. We further examine the role of the death rate in maintaining the system's steady state. Overall, our study sheds light on the strategies employed by stem cells to organize specialized cells and maintain proper functionality. Our findings provide insight into the complex mechanisms involved in tissue development and maintenance, which could lead to new approaches in regenerative medicine and tissue engineering.

Network-Based and Machine-Learning Approaches Identify Diagnostic and Prognostic Models for EMT-Type Gastric Tumors

The microsatellite stable/epithelial-mesenchymal transition (MSS/EMT) subtype of gastric cancer represents a highly aggressive class of tumors associated with low rates of survival and considerably high probabilities of recurrence. In the era of precision medicine, the accurate and prompt diagnosis of tumors of this subtype is of vital importance. In this study, we used Weighted Gene Co-expression Network Analysis (WGCNA) to identify a differentially expressed co-expression module of mRNAs in EMT-type gastric tumors. Using network analysis and linear discriminant analysis, we identified mRNA motifs and microRNA-based models with strong prognostic and diagnostic relevance: three models comprised of (i) the microRNAs miR-199a-5p and miR-141-3p, (ii) EVC/EVC2/GLI3, and (iii) PDE2A/GUCY1A1/GUCY1B1 gene expression profiles distinguish EMT-type tumors from other gastric tumors with high accuracy (Area Under the Receiver Operating Characteristic Curve (AUC) = 0.995, AUC = 0.9742, and AUC = 0.9717; respectively). Additionally, the DMD/ITGA1/CAV1 motif was identified as the top motif with consistent relevance to prognosis (hazard ratio > 3). Molecular functions of the members of the identified models highlight the central roles of MAPK, Hh, and cGMP/cAMP signaling in the pathology of the EMT subtype of gastric cancer and underscore their potential utility in precision therapeutic approaches.

wpLogicNet: logic gate and structure inference in gene regulatory networks

MOTIVATION

The gene regulatory process resembles a logic system in which a target gene is regulated by a logic gate among its regulators. While various computational techniques are developed for a gene regulatory network (GRN) reconstruction, the study of logical relationships has received little attention. Here, we propose a novel tool called wpLogicNet that simultaneously infers both the directed GRN structures and logic gates among genes or transcription factors (TFs) that regulate their target genes, based on continuous steady-state gene expressions.

RESULTS

wpLogicNet proposes a framework to infer the logic gates among any number of regulators, with a low time-complexity. This distinguishes wpLogicNet from the existing logic-based models that are limited to inferring the gate between two genes or TFs. Our method applies a Bayesian mixture model to estimate the likelihood of the target gene profile and to infer the logic gate a posteriori. Furthermore, in structure-aware mode, wpLogicNet reconstructs the logic gates in TF-gene or gene-gene interaction networks with known structures. The predicted logic gates are validated on simulated datasets of TF-gene interaction networks from Escherichia coli. For the directed-edge inference, the method is validated on datasets from E.coli and DREAM project. The results show that compared to other well-known methods, wpLogicNet is more precise in reconstructing the network and logical relationships among genes.

AVAILABILITY AND IMPLEMENTATION

The datasets and R package of wpLogicNet are available in the github repository, https://github.com/CompBioIPM/wpLogicNet.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Removal of Penicillin G from aqueous medium by PPI@SBA-15/ZIF-8 super adsorbent: Adsorption isotherm, thermodynamic, and kinetic studies

In the present paper, synthesis of SBA-15 nanoparticles was carried out from tetraethyl orthosilicate (TEOS) precursor using the sol-gel process. After being combined with Poly propylene imine, and ZIF-8 they were employed for the removal of Penicillin G. The synthesized combination morphology was assessed using nitrogen adsorption and desorption (BET), Fourier transform infrared (FTIR) spectroscopy, and X-ray powder diffraction (XRD). The parameters affecting Penicillin G removal, including pH, amount of adsorbent, time of contact, temperature, and concentration, were optimized, and the optimum levels of the mentioned variables were reported to be pH = 3, 0.03 g, 90 min, 25 °C, and 100 ppm, respectively. In addition, application of Freundlich, Langmuir, Dubinin-Radushkevhch, and Tempkin models and pseudo-first-order and pseudo-second-order adsorption synthetic equations aimed at determining the type of adsorbent isotherm. The results showed that the best fitting of Langmuir (R² = 0.9944, q_m = 400 mg/g) for adsorption isotherm and pseudo-second-order model (R² = 0.9905) for kinetics studies. Furthermore, data of Gibbs free energy and enthalpy demonstrated an exothermic and spontaneous process in the research.

Cohort profile: the ESC EURObservational Research Programme Non-ST-segment elevation myocardial infraction (NSTEMI) Registry

AIMS

The European Society of Cardiology (ESC) EURObservational Research Programme (EORP) Non-ST-segment elevation myocardial infarction (NSTEMI) Registry aims to identify international patterns in NSTEMI management in clinical practice and outcomes against the 2015 ESC Guidelines for the management of acute coronary syndromes in patients presenting without ST-segment-elevation.

METHODS AND RESULTS

Consecutively hospitalised adult NSTEMI patients (n = 3620) were enrolled between 11 March 2019 and 6 March 2021, and individual patient data prospectively collected at 287 centres in 59 participating countries during a two-week enrolment period per centre. The registry collected data relating to baseline characteristics, major outcomes (in-hospital death, acute heart failure, cardiogenic shock, bleeding, stroke/transient ischaemic attack, and 30-day mortality) and guideline-recommended NSTEMI care interventions: electrocardiogram pre- or in-hospital, pre-hospitalization receipt of aspirin, echocardiography, coronary angiography, referral to cardiac rehabilitation, smoking cessation advice, dietary advice, and prescription on discharge of aspirin, P2Y12 inhibition, angiotensin converting enzyme inhibitor (ACEi)/angiotensin receptor blocker (ARB), beta-blocker, and statin.

CONCLUSION

The EORP NSTEMI Registry is an international, prospective registry of care and outcomes of patients treated for NSTEMI, which will provide unique insights into the contemporary management of hospitalised NSTEMI patients, compliance with ESC 2015 NSTEMI Guidelines, and identify potential barriers to optimal management of this common clinical presentation associated with significant morbidity and mortality.

Effect of asymptomatic transmission and emergence time on multi-strain viral disease severity

In a viral epidemic, the emergence of a novel strain with increased transmissibility (larger value of basic reproduction number R₀) sparks the fear that the increase in transmissibility is likely to lead to an increase in disease severity. It is required to investigate if a new, more contagious strain will be necessarily dominant in the population and resulting in more disease severity. In this paper, the impact of the asymptomatic transmission and the emergence time of a more transmissible variant of a multi-strain viral disease on the disease prevalence, disease severity, and the dominant variant in an epidemic was investigated by a proposed 2-strain epidemic model. The simulation results showed that considering only R₀, is insufficient to predict the outcome of a new, more contagious strain in the population. A more transmissible strain with a high fraction of asymptomatic cases can substantially reduce the mortality rate. If the emergence time of the new strain is closer to the start of the epidemic, the new, more contagious variant has more chance to win the viral competition and be the dominant strain; otherwise, despite being more contagious, it cannot dominate previous strains. In conclusion, three factors of R₀, the fraction of asymptomatic transmission, and the emergence time of the new strain are required to correctly determine the prevalence, disease severity, and the winner of the viral competition.

Identification of UBA1 as the causative gene of an X-linked non-Kennedy SBMA

BACKGROUND

Spinal-bulbar muscular atrophy (SBMA; Kennedy's Disease) is a motor neuron disease (MND). Kennedy's Disease is nearly exclusively caused by mutations in the androgen receptor encoding gene (AR). We report results of studies aimed at identification of the genetic cause of a disease that best approximates SBMA in a pedigree (four patients) without mutations in AR.

METHODS

Clinical investigations included thorough neurologic and non-neurologic examinations and testings. Genetic analysis was performed by exome sequencing using standard protocols. UBA1 mutations were modeled on the crystal structure of UBA1.

RESULTS

The clinical features of the patients are described in detail. A missense mutation in UBA1 (c.T1499C; p.Ile500Thr) was identified as the probable cause of the non-Kennedy SBMA in the pedigree. Like AR, UBA1 is positioned on Chromosome X. UBA1 is a highly conserved gene. It encodes ubiquitin like modifier activating enzyme 1 (UBA1) which is the major E1 enzyme of the ubiquitin-proteasome system. Interestingly, UBA1 mutations can also cause infantile-onset X-linked spinal muscular atrophy (XL-SMA). The mutation identified here and the XL-SMA causative mutations were shown to affect amino acids positioned in the vicinity of UBA1's ATP binding site and to cause structural changes.

CONCLUSION

UBA1 was identified as a novel SBMA causative gene. The gene affects protein homeostasis which is one of most important components of the pathology of neurodegeneration. The contribution of this same gene to the etiology of XL-SMA is discussed.

P-388 Isolation and characterization of human uterine fluid lavage-derived extracellular vesicles by three different methods for optimal embryo transfer timing discovery

Study question

What is the suitable method for isolating extracellular vesicles (EVs) from a small volume of Uterine Fluid Lavage (UFL)?

Summary answer

It seems that the qEV column can help in faster, precise, and gentle isolation of EVs from small amounts of UFL.

What is known already

Several studies have discovered that existing EVs in the UFL, which are informative carriers, reflect cytological and molecular conditions of the uterine environment. The relative amounts of the EV components are different in various physiological situations. So, they are the ideal source for precise molecular analysis of the uterine condition to identify the Window of Implantation (WOI) for appropriate embryo transfer (ET) timing. There is limited information describing the most efficient method for EV isolation from a low-volume sample of biological fluids. In particular, EV separation from some biological fluids such as UFL is more complicated because of the viscosity.

Study design, size, duration

The study was conducted in two steps; first, the pre-implantation UFL sampling effect was studied on the implantation and clinical pregnancy rates. UFLs were obtained from 20 IVF Frozen Embryo Transfer (FET) patients as the case group. The control group consisted of 20 FET patients without lavage. In the second step, UFLs (n = 30) were collected and pooled. The EVs were extracted by ultracentrifugation (UC), Sucrose cushion (Suc), and Size-exclusion chromatography (by the qEV column) methods.

Participants/materials, setting, methods

First, UFL was collected two days before frozen blastocyst ET from the case group using an intrauterine insemination catheter attached to a syringe. Then, patients were compared with control at the seventh week. Second, EVs were extracted from pooled UFL samples and characterized by Dynamic Light Scattering (DLS), Scanning Electron Microscopy (SEM), and Western Blot (WB). Albumin contamination was detected by SDS-PAGE. Total RNA was extracted, and Real-time PCR was performed for six housekeeping genes.

Main results and the role of chance

A comparison between case and control groups indicated no significant difference for implantation and clinical pregnancy rates. Moreover, we have confirmed the presence of EVs in UFL that were successfully isolated, by the UC, Suc, the qEV methods. The SEM images showed that the collected vesicles were morphologically spherical. The DLS analysis revealed that the intensity peak of isolated particles with the UC and Suc methods were 281 nm and 216 nm, respectively. Extracted EVs using the qEV technique were smaller and homogenized in size, with an intensity peak of 67.7 nm. SDS-PAGE of EVs showed a weaker albumin band in the qEV column (with a 100 kDa filter) method than the UC, Suc, and qEV column (with a 30 kDa filter) methods. Although, their quantification showed no significant differences. WB analysis indicated common EV markers (D81, CD9, CD63, and TSG101) showed better expression using the qEV extraction technique. But CD9 and TSG101 had lower expression levels in EVs isolated using Suc and UC, respectively. Calnexin was not detected in the isolated EVs. The GAPDH, 18SrRNA, ACTIN, GUSB, HMBS, and YWHAZ genes were detected by real-time PCR in all three EV extraction methods. The 18SrRNA gene showed better CT values.

Limitations, reasons for caution

Uterine fluid samples collection from qualified study groups and the patient’s follow-up for ensuring successful implantation and clinical pregnancy are time-consuming. The low volume of uterine fluid lavage sample and consequently the low number of extracellular vesicles inside it was also the limitation of this study.

Wider implications of the findings

Endometrial receptivity assay is difficult to study non-invasively. Herein, endometrial secretome EVs as a minimally invasive source for uterine environment molecular assessment is presented. High-throughput analysis of EV components can offer biomarkers for individual determination of ET timing, providing an additional method to use with transvaginal-ultrasonography for assessing endometrial receptivity.

Trial registration number

not applicable

A computational model of stem cells' decision-making mechanism to maintain tissue homeostasis and organization in the presence of stochasticity

The maintenance of multi-cellular developed tissue depends on the proper cell production rate to replace the cells destroyed by the programmed process of cell death. The stem cell is the main source of producing cells in a developed normal tissue. It makes the stem cell the lead role in the scene of a fully formed developed tissue to fulfill its proper functionality. By focusing on the impact of stochasticity, here, we propose a computational model to reveal the internal mechanism of a stem cell, which generates the right proportion of different types of specialized cells, distribute them into their right position, and in the presence of intercellular reactions, maintain the organized structure in a homeostatic state. The result demonstrates that the spatial pattern could be harassed by the population geometries. Besides, it clearly shows that our model with progenitor cells able to recover the stem cell presence could retrieve the initial pattern appropriately in the case of injury. One of the fascinating outcomes of this project is demonstrating the contradictory roles of stochasticity. It breaks the proper boundaries of the initial spatial pattern in the population. While, on the flip side of the coin, it is the exact factor that provides the demanded non-genetic diversity in the tissue. The remarkable characteristic of the introduced model as the stem cells' internal mechanism is that it could control the overall behavior of the population without need for any external factors.

AB1528-HPR FULL BODY HAPTIC BODYSUIT - AN INSTRUMENT TO MEASURE THE RANGE AND SPEED OF MOTION IN PATIENTS WITH AXIAL SPONDYLOARTHRITIS (axSpA) - PRELIMINARY RESULTS

Background

Movement of the spine is restricted in axial spondyloarthritis (axSpA) [1]. Spine function is usually assessed by the Bath Ankylosing Spondylitis Metrology Index (BASMI), which is based on a limited set of defined motions that are measured semiquantitatively in the spatial dimension but not in the temporal dimension. Sensor-based measurement of spine function in axSpA patients is in its infancy but may provide a deeper and more detailed understanding of the impact of axSpA on the impairment of spine function [2,3]. In theory, unbiased full body assessment of spine motion may open a new dimension in function analysis in axSpA.

Objectives

To test if a of a full-body based haptic capturing of spine motion is technically feasible and can pick up the measurements of BASMI items 1-5. Furthermore, we aimed to investigate whether such measurements are accurate and reproducible comparing to BASMI scores done by rheumatologists. Lastly, we sought to measure velocity of spine movements to allow spatiotemporal analysis of motion.

Methods

For full-body haptic assessment of spine motion a full-body haptic suit (Teslasuit; VR Electronics Ltd, London) was used that consists of a smart textile two-piece bodysuit that not only captures range and speed of motion but also provides biometric and haptic feedback. This device is currently tested in clinical trials (https://teslasuit.io/rehabilitation/) but has not been tested in rheumatic diseases such as axSpA [4]. Since there is no pre-defined technical solution for measuring BASMI, we used the integrated inertial measurement units (IMUs) of the suit (Figure 1a). The suit is recording the position and rotations of its IMUs and is transforming the raw data to position coordinates and joint angle of the bones. We implemented an algorithm that is accessing the sensor data and is calculating the BASMI measurements as well as velocity. Assessment were done in healthy individuals. BASMI was obtained 3 times by teslasuit followed by standard BASMI measurement by 2 independent rheumatologists. In addition, rotational movements with their maximum torso speed to evaluate angular velocity were performed (Figure 1b). Measurements were compared using absolute values and relative standard deviation (which is the standard deviation normalized by the mean).

Results

Five healthy individuals (all males, age: 27.6 ± 1.8 years, height: 178 ± 5 cm; weight 70.0 ± 8.0 kg) were assessed. Teslasuit measurements were well tolerated. Technically, we were able to calculate BASMI item 3 and 5, finger-to-floor distance and the velocity of the spine movement using the position data of hand, talus and upper back sensors (Figure 1a, b). Due to absence of sensors at the head and the required back areas, BASMI 1, 2, 4 could only partially be captured and require further programming, which is currently performed. Only marginal differences were detected regarding the relative standard deviations of measurements between teslasuit and rheumatologists (BASMI 3: rheumatologists 8,5%: suit 10%; BASMI 5: rheumatologists 5,4%: suit 4,9%) (Figure 1c). The speed of spinal motion could be measured with an average angular velocity of 172.2 degrees/sec over the entire rotation motion and an average maximum angular velocity of 417.2 degrees/sec.

Conclusion

This study shows that full-body haptic-suits can capture spinal motion including parts of the BASMI score. In addition, they allow to measure the speed of spinal movement, which might be an important and so far unrecognized factor to test the impact of axSpA on spinal function. Based on these results, full-body haptic-suits will be tested in axSpA patients in the future. Furthermore, technical solutions are currently developed to implement the remaining BASMI scores into the suit as well as connections from the suit to virtual reality devices for patients and doctors.

References

[1]Sieper, J. and D. Poddubnyy, Axial spondyloarthritis. Lancet 2017.

[2]Gardiner, P.V., et al., Rheumatology (Oxford) 2020.

[3]Kiefer, D., et al., S J Rheumatol 2022.

[4]Caserman, P. et al Sensors (Basel) 2021.

Acknowledgements

This work was (partly) funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – SFB 1483 – Project-ID 442419336, EmpkinS.

Disclosure of Interests

None declared

A randomized controlled clinical trial of the effects of range of motion exercises and massage on muscle strength in critically ill patients

Background

Atrophy and muscle weakness is a common problem in critically ill patients admitted to the intensive care unit (ICU). Muscle weakness in severe cases can lead to tetraplegia, reduced or lost tendon reflexes, delayed weaning from mechanical ventilation, physical disability, and increased mortality. The aim of this study was to compare the effects of range of motion exercises (ROM) and massage on muscle strength of the patients admitted to ICUs.

Methods

This study was a single-blinded randomized controlled trial conducted in ICUs of Afzalipour hospital in Kerman, southeastern Iran. Ninety conscious ICU patients were randomly divided into three groups (massage, ROM exercises and control). The researcher/co-researcher massaged or did ROM exercises on the patients’ extremities once a day for seven consecutive days. Using a hand-held dynamometer, the co-researcher, rated the muscle strength before, on the fourth and seventh days of intervention at 8 p.m.

Results

The mean muscles strength of the right arm in the ROM exercise and massage groups increased by 0.63 kg, and 0.29 kg, respectively after the intervention compared with before the intervention. The muscle strength of the right arm in the control group reduced by 0.55 kg. The mean muscles strength of the left arm in the ROM exercise and massage groups increased by 0.61 kg and 0.28 kg after the intervention, respectively while it reduced by 0.56 kg in the control group. The mean muscles strength of the right leg in the ROM exercise and massage groups increased by 0.53 kg and 0.27 kg after the intervention compared with before the intervention while it reduced by 0.70 kg in the control group. The mean muscles strength of the left leg in the ROM exercise and massage groups increased by 0.54 kg and 0.26 kg after the intervention compared with before the intervention while it reduced by 0.71 kg in the control group.

Conclusion

The results of the present study showed that ROM exercises and massage were effective interventions in increasing muscle strength of the critically ill patients admitted to intensive care units.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13102-022-00489-z.

Internal dosimetry studies of 177Lu-BBN-GABA-DOTA, as a cancer therapy agent, in human tissues based on animal data

The goal of using radiopharmaceuticals for therapeutic purposes is twofold: first, the most damage to cancer cells and, second, the most negligible dose transfers to healthy tissues. As ¹⁷⁷Lu has the potential to cure a wide range of malignancies due to its varied range of beta energies, ¹⁷⁷Lu-BBN-GABA-DOTA has been developed for therapeutic applications. In addition, ¹⁷⁷Lu-BBN-GABA-DOTA can be over-expressed on gastrin-releasing peptide (GRP) receptors of the prostate, breast, small cell lung cancer, gastric, and colon tumors. The purpose of this study was to calculate the amount of dose absorption in human body organs using medical internal radiation dose (MIRD) and GATE code methods, after animal injection. In this study, the amount of absorbed dose in different organs (spleen, kidney, Lung, Pancreas, Heart, Adrenal, Intestine, Stomach, and Liver) were calculated for 1-MBq accumulation of ¹⁷⁷Lu-BBN-GABA-DOTA in source organs (spleen, kidney, Lung, Pancreas, Heart, Adrenal, Intestine, Stomach, and Liver) using Monte Carlo Simulation (GATE code) with Zubal phantom. Moreover, compared with MIRD method, the results of the simulation showed considerable consistency. It was estimated that a 1-MBq administration of ¹⁷⁷Lu-BBN-GABA-DOTA to the human body would result in an absorbed dose of 1.07E-02 mGy and 4.97E-02 (MIRD method) and 1.26E-02 mGy and 5.19E-02 (Gate code) in the Pancreas and adrenal 120 h after injection, respectively. The highest and lowest percentage differences between MIRD and Gate results are related to the Pancreas and spleen, respectively. Finally, the results showed that there is a good agreement between MIRD method and Gate code simulation for absorbed dose estimation.

Determining the adjusted initial treatment dose of warfarin anticoagulant medicine using kernel-based support vector regression

BACKGROUND AND OBJECTIVE

A novel research field in bioinformatics is pharmacogenomics and the corresponding applications of artificial intelligence tools. Pharmacogenomics is the study of the relationship between genotype and responses to medical measures such as drug use. One of the most effective drugs is warfarin anticoagulant, but determining its initial treatment dose is challenging. Mistakes in the determination of the initial treatment dose can result directly in patient death.

METHODS

Some of the most successful techniques for estimating the initial treatment dose are kernel-based methods. However, all the available studies use pre-defined and constant kernels that might not necessarily address the problem's intended requirements. The present study seeks to define and present a new computational kernel extracted from a data set. This process aims to utilize all the data-related statistical features to generate a dose determination tool proportional to the data set with minimum error rate. The kernel-based version of the least square support vector regression estimator was defined. Through this method, a more appropriate approach was proposed for predicting the adjusted dose of warfarin.

RESULTS AND CONCLUSION

This paper benefits from the International Warfarin Pharmacogenomics Consortium (IWPC) Database. The results obtained in this study demonstrate that the support vector regression with the proposed new kernel can successfully estimate the ideal dosage of warfarin for approximately 68% of patients.

Prevalence of ESBL and AmpC genes in E. coli isolates from urinary tract infections in the north of Iran

Beta-lactam resistance in Gram-negative bacteria, especially Escherichia coli, is a main clinical problem. It is often caused by the production of β-lactamases, particularly extended-spectrum β-lactamases (ESBLs) or AmpC enzymes. This study was undertaken to characterize ESBL and AmpC producers among Escherichia coli isolates from urine samples. During six months, 263 E. coli isolates were detected by standard biochemical tests. The isolates were screened for ESBL production by the double-disk synergy test using Ceftazidime (30 μg) and Cefotaxime (30 μg) disks and confirmed by combined disk diffusion test using Clavulanic acid. AmpC production was confirmed by an AmpC disk test based on filter paper disks impregnated with EDTA. The presence of genes encoding TEM, SHV, CTX-M, CIT, FOX, MOX, ACC, and EBC were detected by PCR. 263 E. coli isolates were selected for the combined disk (Ceftazidime, Cefotaxime, and Clavulanic acid) assay in the disk agar diffusion test. In the combined disk assay, among 263 isolates, 121 (46%) isolates were detected as ESBLs, and none of the isolates were AmpC producers. PCR performed on all ESBL producers and blaSHV, blaTEM, and blaCTX-M were detected in 42 (34.7%), 44 (36.4%), and 47 (38.8%) cases, respectively. Also, from 48 Isolates with zone diameters of less than or equal to 18 mm to Cefoxitin, 7 (14.6%), 4 (8.3%), and 9 (18.8%) cases contained MOX, EBC, and CIT genes, respectively. DHA, FOX, and ACC genes were not detected in any sample. Since pathogens evolve in the hospital setting, updating local data, such as this research, offers scientific evidence to improve the outcome of nosocomial infections.

Population-level heterogeneity as a reflection of mixed strategy: A computational perspective on the Crabtree effect

Is population-level heterogeneity a reflection of distinct subpopulations, exhibiting different metabolic functions, or dynamic metabolism of individuals within the population? This fascinating question has remained a subject of great interest in studying metabolic specialization in microorganisms. The Crabtree effect - i.e., the ability of some microorganisms to switch from respiration to fermentation in the presence of oxygen - is an appropriate case study to address the aforementioned question. Game-theoretical approaches have been routinely used to examine and explain the way a microorganism, such as yeast, would switch between the two ATP-producing pathways, i.e., respiration and fermentation. Here we attempt to explain the switch between respiration and fermentation in yeast by constructing a simple metabolic switch. We then utilize an individual-based model, in which each individual is equipped with all the relevant chemical reactions, to see how cells equipped with such metabolic switch would behave in different conditions. We further investigate our proposed metabolic switch using the game-theoretical approach. Based on this model, we postulate that the population-level metabolic heterogeneity in microorganisms can simply arise from individuals utilizing a mixed strategy.

Reactive/Less-cooperative individuals advance population's synchronization: Modeling of Dictyostelium discoideum concerted signaling during aggregation phase

Orchestrated chemical signaling of single cells sounds to be a linchpin of emerging organization and multicellular life form. The social amoeba Dictyostelium discoideum is a well-studied model organism to explore overall pictures of grouped behavior in developmental biology. The chemical waves secreted by aggregating Dictyostelium is a superb example of pattern formation. The waves are either circular or spiral in shape, according to the incremental population density of a self-aggregating community of individuals. Here, we revisit the spatiotemporal patterns that appear in an excitable medium due to synchronization of randomly firing individuals, but with a more parsimonious attitude. According to our model, a fraction of these individuals are less involved in amplifying external stimulants. Our simulations indicate that the cells enhance the system’s asymmetry and as a result, nucleate early sustainable spiral territory zones, provided that their relative population does not exceed a tolerable threshold.

Community-based cardiovascular disease prevention programmes and cardiovascular risk factors: a systematic review and meta-analysis

OBJECTIVES

This study aimed to summarise the effect of community-based intervention programmes on the prevention of cardiovascular disease (CVD) by reducing cardiometabolic risk factors.

STUDY DESIGN

This was a systematic review and meta-analysis.

METHODS

A systematic search in the PubMed database and screening of reference lists aimed to identify community-based CVD prevention programmes from inception up to April 2020. The mean differences and standard deviations for CVD risk factors, including blood pressure, lipid profile, blood glucose and body weight indices, were extracted and pooled using a random effects model.

RESULTS

Screening of 11,889 titles/abstracts and full texts resulted in 48 studies being included in this review. The meta-analysis showed that community-based programmes have led to considerable decreases in systolic blood pressure (weighted mean difference [WMD] = -2.90 mm Hg, 95% confidence interval [95% CI]: -3.63, -2.16), diastolic blood pressure (WMD = -2.21 mm Hg, 95% CI: -3.12, -1.29), serum levels of low-density lipoprotein cholesterol (LDL-C; WMD = -8.88 mg/dl, 95% CI: -12.84, -4.92), triglycerides (WMD = -8.40 mg/dl, 95% CI: -12.10, -4.70), total cholesterol (WMD = -2.96 mg/dl, 95% CI: -3.10, -2.81) and fasting blood glucose (WMD = -2.06 mg/dl, 95% CI: -3.02, -1.10). A moderate decrease in body weight was also found with community-based CVD prevention programmes. However, community-based CVD prevention programmes were not associated with any significant changes in serum levels of high-density lipoprotein.

CONCLUSIONS

The present study indicates that community-based strategies have successfully led to an improvement in CVD risk factors, particularly by reducing blood pressure, serum levels of LDL-C and triglycerides, obesity indices and blood glucose. The impact of these programmes on CVD is modified by the type of intervention and by different cultural and physical environments.

Orexin-2 receptor antagonism in the cornu ammonis 1 region of hippocampus prevented the antinociceptive responses induced by chemical stimulation of the lateral hypothalamus in the animal model of persistent pain

Orexins are excitatory neuropeptides, mainly produced by neurons located in the lateral hypothalamus, which project to many brain areas. The orexinergic system plays a fundamental role in arousal, sleep/wakefulness, feeding, energy homeostasis, motivation, reward, stress and pain modulation. As a prominent part of the limbic system, the hippocampus has been involved in formalin-induced nociception modulation. Moreover, hippocampus regions express both orexin-1 (OX1) and orexin-2 (OX2) receptors. The present study investigated the role of OX2 receptors (OX2R) within the cornu ammonis 1 (CA1) region of the hippocampus in the mediation of lateral hypothalamus-induced antinociception. Fifty-three male Wistar rats were unilaterally implanted with two separate cannulae into the lateral hypothalamus and CA1. Animals were pretreated with intra-CA1 TCS OX2 29 as an OX2R antagonist before intra-lateral hypothalamus administration of carbachol (250 nM) as a muscarinic agonist for chemical stimulation of orexinergic neurons. Formalin test was used as an animal model of persistent pain, following intra-lateral hypothalamus carbachol microinjection. Results showed that the chemical stimulation of the lateral hypothalamus significantly attenuated formalin-evoked nociceptive behaviors during both phases of the formalin test, and administration of TCS OX2 29 into the CA1 blocked these antinociceptive responses in both phases, especially in the late phase. These findings suggest that OX2 receptors in the CA1 partially mediate the lateral hypothalamus-induced antinociceptive responses in persistent inflammatory pain.

Evaluation of the GABAA Receptor Expression and the Effects of Muscimol on the Activity of Wide Dynamic Range Neurons Following Chronic Constriction Injury of Sciatic Nerve in Rats

Introduction

The modality of γ-aminobutyric acid type a receptors (GABAA) controls dorsal horn neuronal excitability and inhibits sensory information. This study aimed to investigate the expression of the GABAA receptor and the effects of its agonist muscimol on Wide Dynamic Range (WDR) neuronal activity in the Chronic Constriction Injury (CCI) model of neuropathic pain.

Methods

Adult male Wistar rats weighing 200 to 250 g were used to induce CCI neuropathy. Fourteen days after surgery, muscimol (0.5, 1, and 2 mg/kg IP) was injected. Then, the behavioral tests were performed. After that, the animals were killed, and the lumbar segments of the spinal cords were collected for Western blot analysis of the GABAA receptor α1 subunit expression. The electrophysiological properties of WDR neurons were studied by single-unit recordings in separate groups 14 days after CCI.

Results

The outcomes indicated the development of thermal hyperalgesia and mechanical allodynia after neuropathy; nonetheless, the expression of the GABAA receptor α1 subunit did not change significantly. Moreover, the evoked responses of the WDR neurons to electrical, mechanical, and thermal stimuli increased considerably. Fourteen days after CCI, muscimol administration decreased thermal hyperalgesia, mechanical allodynia, and hyper-responsiveness of the WDR neurons in CCI rats.

Conclusion

The modulation of the spinal GABAA receptors after nerve injury can offer further insights to design new therapeutic agents to reduce neuropathic pain symptoms.

Prospects and challenges of cancer systems medicine: from genes to disease networks

It is becoming evident that holistic perspectives toward cancer are crucial in deciphering the overwhelming complexity of tumors. Single-layer analysis of genome-wide data has greatly contributed to our understanding of cellular systems and their perturbations. However, fundamental gaps in our knowledge persist and hamper the design of effective interventions. It is becoming more apparent than ever, that cancer should not only be viewed as a disease of the genome but as a disease of the cellular system. Integrative multilayer approaches are emerging as vigorous assets in our endeavors to achieve systemic views on cancer biology. Herein, we provide a comprehensive review of the approaches, methods and technologies that can serve to achieve systemic perspectives of cancer. We start with genome-wide single-layer approaches of omics analyses of cellular systems and move on to multilayer integrative approaches in which in-depth descriptions of proteogenomics and network-based data analysis are provided. Proteogenomics is a remarkable example of how the integration of multiple levels of information can reduce our blind spots and increase the accuracy and reliability of our interpretations and network-based data analysis is a major approach for data interpretation and a robust scaffold for data integration and modeling. Overall, this review aims to increase cross-field awareness of the approaches and challenges regarding the omics-based study of cancer and to facilitate the necessary shift toward holistic approaches.

Network analysis and the impact of Aflibercept on specific mediators of angiogenesis in HUVEC cells

Angiogenesis, inflammation and endothelial cells’ migration and proliferation exert fundamental roles in different diseases. However, more studies are needed to identify key proteins and pathways involved in these processes. Aflibercept has received the approval of the US Food and Drug Administration (FDA) for the treatment of wet AMD and colorectal cancer. Moreover, the effect of Aflibercept on VEGFR2 downstream signalling pathways has not been investigated yet. Here, we integrated text mining data, protein‐protein interaction networks and multi‐experiment microarray data to specify candidate genes that are involved in VEGFA/VEGFR2 signalling pathways. Network analysis of candidate genes determined the importance of the nominated genes via different centrality parameters. Thereupon, several genes—with the highest centrality indexes—were recruited to investigate the impact of Aflibercept on their expression pattern in HUVEC cells. Real‐time PCR was performed, and relative expression of the specific genes revealed that Aflibercept modulated angiogenic process by VEGF/PI3KA/AKT/mTOR axis, invasion by MMP14/MMP9 axis and inflammation‐related angiogenesis by IL‐6‐STAT3 axis. Data showed Aflibercept simultaneously affected these processes and determined the nominated axes that had been affected by the drug. Furthermore, integrating the results of Aflibercept on expression of candidate genes with the current network analysis suggested that resistance against the Aflibercept effect is a plausible process in HUVEC cells.

False Negative Mitigation in Group Testing for COVID-19 Screening

After lifting the COVID-19 lockdown restrictions and opening businesses, screening is essential to prevent the spread of the virus. Group testing could be a promising candidate for screening to save time and resources. However, due to the high false-negative rate (FNR) of the RT-PCR diagnostic test, we should be cautious about using group testing because a group's false-negative result identifies all the individuals in a group as uninfected. Repeating the test is the best solution to reduce the FNR, and repeats should be integrated with the group-testing method to increase the sensitivity of the test. The simplest way is to replicate the test twice for each group (the 2Rgt method). In this paper, we present a new method for group testing (the groupMix method), which integrates two repeats in the test. Then we introduce the 2-stage sequential version of both the groupMix and the 2Rgt methods. We compare these methods analytically regarding the sensitivity and the average number of tests. The tradeoff between the sensitivity and the average number of tests should be considered when choosing the best method for the screening strategy. We applied the groupMix method to screening 263 people and identified 2 infected individuals by performing 98 tests. This method achieved a 63% saving in the number of tests compared to individual testing. Our experimental results show that in COVID-19 screening, the viral load can be low, and the group size should not be more than 6; otherwise, the FNR increases significantly. A web interface of the groupMix method is publicly available for laboratories to implement this method.

Optogenetic control of neural differentiation in Opto-mGluR6 engineered retinal pigment epithelial cell line and mesenchymal stem cells

In retinal degenerative disorders, when neural retinal cells are damaged, cell transplantation is one of the most promising therapeutic approaches. Optogenetic technology plays an essential role in the neural differentiation of stem cells via membrane depolarization. This study explored the efficacy of blue light stimulation in neuroretinal differentiation of Opto-mGluR6-engineered mouse retinal pigment epithelium (mRPE) and bone marrow mesenchymal stem cells (BMSCs). mRPE and BMSCs were selected for optogenetic study due to their capability to differentiate into retinal-specific neurons. BMSCs were isolated and phenotypically characterized by the expression of mesenchymal stem cell-specific markers, CD44 (99%) and CD105 (98.8%). mRPE culture identity was confirmed by expression of RPE-specific marker, RPE65, and epithelial cell marker, ZO-1. mRPE cells and BMSCs were transduced with AAV-MCS-IRES-EGFP-Opto-mGluR6 viral vector and stimulated for 5 days with blue light (470 nm). RNA and protein expression of Opto-mGluR6 were verified. Optogenetic stimulation-induced elevated intracellular Ca²⁺ levels in mRPE- and BMS-treated cells. Significant increase in cell growth rate and G1/S phase transition were detected in mRPE- and BMSCs-treated cultures. Pou4f1, Dlx2, Eomes, Barlh2, Neurod2, Neurod6, Rorb, Rxrg, Nr2f2, Ascl1, Hes5, and Sox8 were overexpressed in treated BMSCs and Barlh2, Rorb, and Sox8 were overexpressed in treated mRPE cells. Expression of Rho, Thy1, OPN1MW, Recoverin, and CRABP, as retinal-specific neuron markers, in mRPE and BMS cell cultures were demonstrated. Differentiation of ganglion, amacrine, photoreceptor cells, and bipolar and Muller precursors were determined in BMSCs-treated culture and were compared with mRPE. mRPE cells represented more abundant terminal Muller glial differentiation compared with BMSCs. Our results also demonstrated that optical stimulation increased the intracellular Ca²⁺ level and proliferation and differentiation of Opto-mGluR6-engineered BMSCs. It seems that optogenetic stimulation of mRPE- and BMSCs-engineered cells would be a potential therapeutic approach for retinal degenerative disorders.

Effect of lateral crural cut overlay and medial crural cut and overlay in creating and maintaining tip projection and rotation: a randomised single-blind trial

Lateral crural cut and overlay (LCC) or medial crural cut and overlay (MCC) are two of the many techniques applied to ensure an adequate nasal tip projection and rotation, but little evidence supports their long-term efficacy. Fifty-four rhinoplasty candidates were studied prospectively in this randomised clinical trial. The subjects were randomly divided into two groups according to the use of LCC or MCC. The outcome measures were gaining and maintaining tip projection and rotation in the long term. Standardised photographs taken before and at three and 12 months after surgery were used to compare nasolabial angle and projection between groups. Patients' satisfaction with the cosmetic results and nasal obstruction were evaluated using the Standardised Cosmesis and Health Nasal Outcomes Survey (SCHNOS). LCC and MCC were each used in 26 cases. Preoperatively, the nasolabial angle, tip projection, and other characteristics were not significantly different between the groups. There was no significant difference in tip rotation stability (p = 0.624) and projection (p = 0.329) between the groups postoperatively, but patients' satisfaction with the cosmetic results was significantly higher in the MCC group (p = 0.046). It seems that both LCC and MCC are effective techniques in rhinoplasty. Compared with LCC, the use of MCC in qualified hands may increase the patients' satisfaction with the cosmetic results.

Effect of Isoflurane versus Propofol on the Early Outcome of Living Donor Adult Kidney Transplantation

Background

Optimizing anesthetic management for the best possible outcome is essential in kidney transplantation (KT).

Objective

To evaluate the difference in grafted kidney function and early kidney transplant outcome when the pairs of donor-recipient were anesthetized with isoflurane compared to propofol.

Methods

Thirty-eight pairs of kidney transplant donor-recipient were anesthetized with isoflurane, and 22 pairs were anesthetized with propofol. Blood urea nitrogen (BUN), serum creatinine (SCr), estimated glomerular filtration rate (eGFR) were assessed in the preoperative period, on the first postoperative day, before discharge from the hospital, and 6 months after KT. Short-term (6 months) outcomes of KT were assessed by the incidence of delayed graft function, acute rejection episodes, and graft failure.

Results

There was no statistically significant difference between the two groups in the serial measurements of SCr, BUN, eGFR, and the early outcomes (6 months) after surgery. Interestingly, donor warm ischemic time in the propofol group was significantly longer than in the isoflurane group (4.05±1.02, 2.93±0.87 minutes, respectively) (p=0.001). Moreover, postoperative hospital stay in the propofol group were significantly shorter compared to the isoflurane group (9.63±2.96, 11.78±4.91 days, respectively) (p=0.02).

Conclusion

There were no significant differences in transplanted kidney function and the early outcome of kidney transplantation between the two study groups. However, earlier hospital discharge after surgery in the propofol group suggests that propofol may be a more appropriate anesthetic choice in these patients.

Occurrence and Fate of Amoxicillin and Penicillin G Antibiotics in Hospital Wastewater Treatment Plants: A Case Study - Gonbad Kavous, Iran

ABSTRACT Release of antibiotics to the environment as a result of wastewater effluent discharge is a cause for concern worldwide, as they pose a potential threat to human health and the earth ecosystem. Penicillin and amoxicillin are widely used antibiotics. Despite their rapid hydrolysis in aqueous matrices, their presence in the environment is widely investigated. The current study reported and analysed the current state of four hospital wastewater treatment plants (WWTPs) in Gonbad Kavous, Iran, during 2019, from the perspective of amoxicillin and penicillin G removals. WWTPs were sampled at various stages of the treatment process to determine at which stage the antibiotics are being removed. Concentrations of amoxicillin and penicillin G in raw wastewater, analysed by HPLC, varied from 0.35 to 1.02 and 0.02-0.31 /AgL-1, respectively. These values reduced in the final effluent, corresponding to overall efficiency in removing the studied antibiotics of 20-60.5%. Anaerobic processes (i.e. septic tank) slightly outperformed aerobic biological processes for both antibiotics' removal, and penicillin G was removed more efficiently than amoxicillin. Effects of wastewater physicochemical properties, including chemical oxygen demand (COD), biochemical oxygen demand (BOD), and total suspended solids (TSS) on antibiotics removal, were also studied. Whereas statistically significant correlations were noticed between COD, amoxicillin and penicillin G removals, their decline showed no correlation with TSS removal. Our study shows that despite the deployment of treatment plants, a considerable amount of antibiotics is released into receiving water bodies, resulting in significant amounts of these pharmaceuticals entering the environment. There is abundant room for further progress in the detection and quantification of pharmaceuticals and other emerging contaminants in hospital wastewaters and their metabolites and biodegradation products. Keywords: amoxicillin; penicillin G; high-performance liquid chromatography; hospital wastewater treatment plants; removal.

Inter-protein residue covariation information unravels physically interacting protein dimers

BACKGROUND

Predicting physical interaction between proteins is one of the greatest challenges in computational biology. There are considerable various protein interactions and a huge number of protein sequences and synthetic peptides with unknown interacting counterparts. Most of co-evolutionary methods discover a combination of physical interplays and functional associations. However, there are only a handful of approaches which specifically infer physical interactions. Hybrid co-evolutionary methods exploit inter-protein residue coevolution to unravel specific physical interacting proteins. In this study, we introduce a hybrid co-evolutionary-based approach to predict physical interplays between pairs of protein families, starting from protein sequences only.

RESULTS

In the present analysis, pairs of multiple sequence alignments are constructed for each dimer and the covariation between residues in those pairs are calculated by CCMpred (Contacts from Correlated Mutations predicted) and three mutual information based approaches for ten accessible surface area threshold groups. Then, whole residue couplings between proteins of each dimer are unified into a single Frobenius norm value. Norms of residue contact matrices of all dimers in different accessible surface area thresholds are fed into support vector machine as single or multiple feature models. The results of training the classifiers by single features show no apparent different accuracies in distinct methods for different accessible surface area thresholds. Nevertheless, mutual information product and context likelihood of relatedness procedures may roughly have an overall higher and lower performances than other two methods for different accessible surface area cut-offs, respectively. The results also demonstrate that training support vector machine with multiple norm features for several accessible surface area thresholds leads to a considerable improvement of prediction performance. In this context, CCMpred roughly achieves an overall better performance than mutual information based approaches. The best accuracy, sensitivity, specificity, precision and negative predictive value for that method are 0.98, 1, 0.962, 0.96, and 0.962, respectively.

CONCLUSIONS

In this paper, by feeding norm values of protein dimers into support vector machines in different accessible surface area thresholds, we demonstrate that even small number of proteins in pairs of multiple alignments could allow one to accurately discriminate between positive and negative dimers.

A Network-Based Comparison Between Molecular Apocrine Breast Cancer Tumor and Basal and Luminal Tumors by Joint Graphical Lasso

Joint graphical lasso (JGL) approach is a Gaussian graphical model to estimate multiple graphical models corresponding to distinct but related groups. Molecular apocrine (MA) breast cancer tumor has similar characteristics to luminal and basal subtypes. Due to the relationship between MA tumor and two other subtypes, this paper investigates the similarities and differences between the MA genes association network and the ones corresponding to other tumors by taking advantageous of JGL properties. Two distinct JGL graphical models are applied to two sub-datasets including the gene expression information of the MA and the luminal tumors and also the MA and the basal tumors. Then, topological comparisons between the networks such as finding the shared edges are applied. In addition, several support vector machine (SVM) classification models are performed to assess the discriminating power of some critical nodes in the networks, like hub nodes, to discriminate the tumors sample. Applying the JGL approach prepares an appropriate tool to observe the networks of the MA tumor and other subtypes in one map. The results obtained by comparing the networks could be helpful to generate new insight about MA tumor for future studies.

A computational model of stem cell molecular mechanism to maintain tissue homeostasis

Stem cells, with their capacity to self-renew and to differentiate to more specialized cell types, play a key role to maintain homeostasis in adult tissues. To investigate how, in the dynamic stochastic environment of a tissue, non-genetic diversity and the precise balance between proliferation and differentiation are achieved, it is necessary to understand the molecular mechanisms of the stem cells in decision making process. By focusing on the impact of stochasticity, we proposed a computational model describing the regulatory circuitry as a tri-stable dynamical system to reveal the mechanism which orchestrate this balance. Our model explains how the distribution of noise in genes, linked to the cell regulatory networks, affects cell decision-making to maintain homeostatic state. The noise effect on tissue homeostasis is achieved by regulating the probability of differentiation and self-renewal through symmetric and/or asymmetric cell divisions. Our model reveals, when mutations due to the replication of DNA in stem cell division, are inevitable, how mutations contribute to either aging gradually or the development of cancer in a short period of time. Furthermore, our model sheds some light on the impact of more complex regulatory networks on the system robustness against perturbations.

LogicNet: probabilistic continuous logics in reconstructing gene regulatory networks

Background

Gene Regulatory Networks (GRNs) have been previously studied by using Boolean/multi-state logics. While the gene expression values are usually scaled into the range [0, 1], these GRN inference methods apply a threshold to discretize the data, resulting in missing information. Most of studies apply fuzzy logics to infer the logical gene-gene interactions from continuous data. However, all these approaches require an a priori known network structure.

Results

Here, by introducing a new probabilistic logic for continuous data, we propose a novel logic-based approach (called the LogicNet) for the simultaneous reconstruction of the GRN structure and identification of the logics among the regulatory genes, from the continuous gene expression data. In contrast to the previous approaches, the LogicNet does not require an a priori known network structure to infer the logics. The proposed probabilistic logic is superior to the existing fuzzy logics and is more relevant to the biological contexts than the fuzzy logics. The performance of the LogicNet is superior to that of several Mutual Information-based and regression-based tools for reconstructing GRNs.

Conclusions

The LogicNet reconstructs GRNs and logic functions without requiring prior knowledge of the network structure. Moreover, in another application, the LogicNet can be applied for logic function detection from the known regulatory genes-target interactions. We also conclude that computational modeling of the logical interactions among the regulatory genes significantly improves the GRN reconstruction accuracy.

Phylogenetic and phylodynamic study of Human T-cell lymphotropic virus Type 1 (HTLV-1) in Iran

Human T-lymphotropic virus type-1 (HTLV-1) is a retrovirus that causes the neurological disorder HTLV-1 associated myelopathy/ tropical spastic paraparesis (HAM/TSP) and/or adult T-cell leukemia/lymphoma (ATLL). Iran is one of the endemic regions of the HTLV-1 in the Middle East. To infer the origin of the virus in Iran and to follow the movements of human population and routes of virus spread to this country, phylogenetic and phylodynamic analyses were performed. To this purpose, the long terminal repeat (LTR) region of HTLV-1 was used. New LTR sequences were obtained from 100 blood samples which infected with HTLV-1. Moreover, all Iranian LTR sequences which have been reported so far, were obtained from GenBank database. Sequences were aligned and maximum-likelihood and Bayesian tree topologies were explored. After identification of Iranian specific cluster, molecular-clock and coalescent models were used to estimate time to the most recent common ancestor (tMRCA). Bayesian Skyline Plots (BSP), representing population dynamics HTLV-1 strains back to the MRCA, were estimated using BEAST software. Phylogenetic analysis demonstrated that the Iranian, Kuwaiti, German, Israelite and southern Indian isolates are located within the widespread "transcontinental" subgroup A clade of HTLV-1 Cosmopolitan subtype a. Molecular clock analysis of the Iranian cluster dated back their respective tMRCA to be 1290 AC with a 95% HPD confidence intervals (918, 1517). BSPs indicated a rapid exponential growth rate in the effective number of infections prior the 15th century. Our results support the hypothesis of a multiple introductions of HTLV-1 into Iran with the majority of introductions occurring in prior the 15th century, at the same time the Mongol invasion of Iran. Our results further suggest that HTLV-1 introduction into Iran was facilitated by the commercial/migratory linkage as known as the ancient Silk Road which linked China to Antioch (now in Turkey).

Feedback-based Self-improving CNN Algorithm for Breast Cancer Lymph Node Metastasis Detection in Real Clinical Environment

Digital pathology can be thought of as a model composed of 3 main elements; classification algorithm, Graphical User Interface (GUI) and the pathologists. Currently there is only a one way interaction from the classification algorithm to the pathologist. This paper, proposes an additional backward path which is a new feedback-based method, aimed to improve the performance of the classification algorithms by utilizing the feedback of the pathologists. The GUI developed for this purpose, is aimed to be simple and adaptive to different classification algorithms. The method showed significant improvement in the classification performance of the applied Convolutional Neural Network (CNN) algorithm. The 25% quantile of the probability score of the predictions increased from 0.48 to 0.89 and the median of the data increased from 0.95 to 0.99.

Noise-driven cell differentiation and the emergence of spatiotemporal patterns

The emergence of phenotypic diversity in a population of cells and their arrangement in space and time is one of the most fascinating features of living systems. In fact, understanding multicellularity is unthinkable without explaining the proximate and the ultimate causes of cell differentiation in time and space. Simpler forms of cell differentiation can be found in unicellular organisms, such as bacterial biofilm, where reversible cell differentiation results in phenotypically diverse populations. In this manuscript, we attempt to start with the simple case of reversible nongenetic phenotypic to construct a model of differentiation and pattern formation. Our model, which we refer to as noise-driven differentiation (NDD) model, is an attempt to consider the prevalence of noise in biological systems, alongside what is known about genetic switches and signaling, to create a simple model which generates spatiotemporal patterns from bottom-up. Our simulations indicate that the presence of noise in cells can lead to reversible differentiation and the addition of signaling can create spatiotemporal pattern.

Mid-infrared hybrid Si/VO2 modulator electrically driven by graphene electrodes

Silicon photonic platforms are of significant interest for a variety of applications that operate in the mid-infrared regime. However, the realization of efficient mid-IR modulators, key components in any integrated optics platform, is still a challenging topic. Here, an ultra-compact high-speed hybrid Si/VO₂ modulator operating at a mid-IR wavelength of 3.8 μm is presented. Electrical properties of graphene are employed to achieve a reversible insulating-metal phase transition in VO₂ by electrical actuation. The thermal characteristics of graphene are employed to improve the response time of the VO₂ phase transition through speed up heating and dissipation processes, thus enhancing the modulation speed. Optical and thermal simulations show an extinction ratio of 4.4 dB/μm, an insertion loss of 0.1 dB/μm, and high modulation speed of 23 ns. A larger modulation depth as high as 10 dB/μm can be achieved at the cost of lower modulation speed.

Integrative Analysis of Breast Cancer Cells Reveals an Epithelial-Mesenchymal Transition Role in Adaptation to Acidic Microenvironment

Early ducts of breast tumors are unequivocally acidic. High rates of glycolysis combined with poor perfusion lead to a congestion of acidic metabolites in the tumor microenvironment, and pre-malignant cells must adapt to this acidosis to thrive. Adaptation to acidosis selects cancer cells that can thrive in harsh conditions and are capable of outgrowing the normal or non-adapted neighbors. This selection is usually accompanied by phenotypic change. Epithelial mesenchymal transition (EMT) is one of the most important switches correlated to malignant tumor cell phenotype and has been shown to be induced by tumor acidosis. New evidence shows that the EMT switch is not a binary system and occurs on a spectrum of transition states. During confirmation of the EMT phenotype, our results demonstrated a partial EMT phenotype in our acid-adapted cell population. Using RNA sequencing and network analysis we found 10 dysregulated network motifs in acid-adapted breast cancer cells playing a role in EMT. Our further integrative analysis of RNA sequencing and SILAC proteomics resulted in recognition of S100B and S100A6 proteins at both the RNA and protein level. Higher expression of S100B and S100A6 was validated in vitro by Immunocytochemistry. We further validated our finding both in vitro and in patients' samples by IHC analysis of Tissue Microarray (TMA). Correlation analysis of S100A6 and LAMP2b as marker of acidosis in each patient from Moffitt TMA approved the acid related role of S100A6 in breast cancer patients. Also, DCIS patients with higher expression of S100A6 showed lower survival compared to lower expression. We propose essential roles of acid adaptation in cancer cells EMT process through S100 proteins such as S100A6 that can be used as therapeutic strategy targeting both acid-adapted and malignant phenotypes.

The effect of dietary coenzyme Q10 on plasma metabolites and hepatic gene expression in broiler breeder hens

1. This study was performed to evaluate the effects of dietary supplementation of coenzyme Q10 (CoQ10) on laying rate, body weight, plasma metabolites and some liver gene expression in broiler breeder hens. 2. A total of 128 broiler breeder hens (Arbor Acres Plus, 47 weeks of age) were randomly distributed to four dietary groups supplemented with different levels of CoQ10 (0, 300, 600 or 900 mg/kg diet) with four replicates of eight hens each. During 47-54 weeks of age, laying rate, egg mass and body weight were recorded weekly. To assay plasma biochemical indicators, blood samples were collected at 54 weeks of age. At the end of the experiment, for evaluating the abdominal fat weight, liver weight and expression of the adiponectin and proliferator-activated receptor-α (PPAR-α) genes in the liver, eight hens per treatment were selected, weighed and humanely killed by decapitation. 3. Dietary supplementation of CoQ10 linearly decreased abdominal fat weight, alanine aminotransferase (ALT) and aspartate aminotransferase (AST) activities by increased levels of CoQ10. The plasma levels of glucose, cholesterol and alkaline phosphatase (ALP) activity were quadratically decreased by increased levels of CoQ10. The best plasma levels of glucose, cholesterol and ALP activity were estimated at 562.5, 633.3 and 517.8 mg CoQ10/kg diet, respectively. Adiponectin and PPARα gene expression exhibited a linear increased by increased levels of CoQ10. 4. In conclusion, addition of CoQ10 to the diet influenced lipid metabolism and expression of the adiponectin and PPAR-α genes, which might be partially due to the improvement in mitochondrial metabolism and energy production. However, further studies are necessary to determine the effects of CoQ10 on these indicators in broiler breeder hens during ageing.

Enhanced quasi-phase-matched second-harmonic generation in a silicon-organic hybrid microring resonator

An enhanced second-harmonic generation process in a dually resonant silicon-organic hybrid microring resonator is presented. The necessary phase matching is fulfilled through quasi-phase matching by periodically altering the spatial distribution of the second-order nonlinearity ${\chi ^{(2)}}$χ⁽²⁾ of polymer infiltrated into a slot layer along the microring resonator propagation length. Absolute conversion efficiency up to ${P_{2\omega }}/{P_\omega } = {38}\% $P_2ω/P_ω=38% with only 10 mW pump power at $\lambda = 3.1\;{\unicode{x00B5}{\rm m}}$λ=3.1µm is obtained in an optimized structure, which shows a ${\sim}{76}$∼76-fold improvement compared to that of the straight waveguide. Also, our efficiency is comparable to that of previous works, even with the much lower pump power. We expect that our device will provide a potential application for bridging the mid-infrared and near-infrared bands on silicon photonics platforms.