Integration of machine learning models with microsatellite markers: New avenue in world grapevine germplasm characterization.

Development of efficient analytical techniques is required for effective interpretation of biological data to take novel hypotheses and finding the critical predictive patterns. Machine Learning algorithms provide a novel opportunity for development of low-cost and practical solutions in biology. In this study, we proposed a new integrated analytical approach using supervised machine learning algorithms and microsatellites data of worldwide vitis populations. A total of 1378 wild (V. vinifera spp. sylvestris) and cultivated (V. vinifera spp. sativa) accessions of grapevine were investigated using 20 microsatellite markers. Data cleaning, feature selection, and supervised machine learning classification models vis, Naive Bayes, Support Vector Machine (SVM) and Tree Induction methods were implied to find most indicative and diagnostic alleles to represent wild/cultivated and originated geography of each population. Our combined approaches showed microsatellite markers with the highest differentiating capacity and proved efficiency for our pipeline of classification and prediction of vitis accessions. Moreover, our study proposed the best combination of markers for better distinguishing of populations, which can be exploited in future germplasm conservation and breeding programs.

Trancriptome data mining in combination with co-expression network analysis identifies the functional modules and critical regulators in Hordeum vulgare L. in response to cold stress.

Cold stress, as an abiotic stress, is one of the most limiting factors which pose a great threat to the plant's productivity. To understand the transcriptional regulation and connectivity pattern of genes involved in barley cold stress responses, co-expression network analysis was performed based on the global transcriptome profiling. The microarray datasets related to cold stress treatments were retrieved from the Gene Expression Omnibus (GEO) and Array express databases. Four microarray datasets related to cold stress-responsive transcriptome in barley were included in our study. Gene co-expression analysis was constructed using WGCNA method. Module-Trait Relationships (MTR) analysis and hub genes determination and validation were carried out. Finally, transcription factor and kinase regulatory networks were Inferred using machine learning algorithm. The co-expression modules were determined using beta index = 10. In total 13 co-expressed modules were identified with an average size of 153 genes. Functional enrichment based on gene ontology (GO) showed that each of the stress related significant modules were enriched in different biological processes. Annotation of significant modules identifies some TFs and Kinases such as ethylene-responsive transcription factor 1-like, transcription factor PCL1-like, transcription factor MYC2, WRKY, serine/threonine-protein kinase PBL7, and receptor-like protein kinase At2g42960 were contributed in barley cold stress response. Our analysis highlighted the functional importance of ABA signaling pathway, ROS signaling, defensive and protective proteins, degrading protein, Ca2+ related signaling, ribosome-mediated translation and etc. in responding of barley to cold stress condition. The current findings add substantially to our understanding of the cold responsive underlying mechanism of barley which can serve in future studies and breeding programs.

Safety of dual antiplatelet therapy in the acute phase of aneurysmal subarachnoid hemorrhage: a propensity score-matched study.

OBJECTIVE: With the evolution of neuroendovascular treatments, there is a great trend to treat acutely ruptured wide-necked aneurysms with stent-assisted coiling (SAC) and flow diverters (FDs), which inevitably requires dual antiplatelet therapy (DAPT). This therapy can increase the rate of hemorrhagic complications following other neurosurgical maneuvers, such as external ventricular drain (EVD) placement or removal. In this study, the authors aimed to evaluate the safety of DAPT in patients with aneurysmal subarachnoid hemorrhage (SAH) treated with SAC or FDs and the therapy's potential benefit in reducing cerebral ischemia and cerebral vasospasm. METHODS: In this retrospective study, the authors reviewed the records of patients who had been admitted to their hospital with acute aneurysmal SAH and treated with SAC, FDs, and/or coiling between 2012 and 2022. Patients were classified into two groups: a DAPT group, including patients who had received DAPT for SAC or FDs, and a non-DAPT group, including patients who had not received any antiplatelet regimen and had been treated with coiling. Perioperative hemorrhagic and ischemic complications and clinical outcomes were compared between the two groups. RESULTS: From among 938 cases of acute ruptured aneurysms treated during 10 years of study, 192 patients were included in this analysis, with 96 patients in each treatment group, after propensity score matching. All basic clinical and imaging characteristics were equivalent between the two groups except for the neck size of aneurysms (p < 0.001). EVD-related hemorrhage was significantly higher in the DAPT group than in the non-DAPT group (p = 0.035). In most patients, however, the EVD-related hemorrhage was insignificant. Parent artery or stent-induced thrombosis was higher in the DAPT group than in the non-DAPT group (p = 0.003). The rate of cerebral ischemia was slightly lower in the DAPT group than in the non-DAPT group (11.5% vs 15.6%, p = 0.399). In the multivariate analysis, cerebral ischemia, rebleeding before securing the aneurysm, extracranial hemorrhage, and cerebral vasospasm were the predictive factors of a poor clinical outcome (p < 0.001, p < 0.001, p = 0.038, and p = 0.038, respectively). CONCLUSIONS: The DAPT regimen may be safe in the setting of acute aneurysmal SAH. Although EVD-related hemorrhage is more common in the DAPT group than the non-DAPT group, it is usually insignificant without any neurological deficit.

A stepwise approach to prescribing novel lipid-lowering medications.

Dyslipidemia is a major modifiable risk factor for developing atherosclerotic cardiovascular disease. Despite increasing high intensity statin prescription and adherence to statin therapy, a considerable number of patients will not reach the guideline directed goals due to statin intolerance, lack of adherence or treatment efficacy. Several new lipid lowering medications have received approval by regulatory agencies in the past decade including proprotein convertase subtilisin/kexin type 9 modulators, ATP-citrate lyase inhibitors, angiopoietin-like 3 inhibitors, lomitapide, and icosapent ethyl. Although approved by regulatory agencies, these medications are still under-prescribed worldwide which may be related to cost issues, lack of cardiovascular outcome results, or clinicians not being familiar with their use. In this review, we propose a practical stepwise approach including each class' efficacy, place in therapy, adverse effects, warnings and precautions, and monitoring parameters. This information can help the clinicians to prescribing these novel lipid lowering medications to achieve treatment goals and reduce the risk of atherosclerotic cardiovascular disease. The aim is to shift the paradigm for high-intensity statins from watch and wait to initial combination therapy for high-risk patients.

Quantitative structure-activity relationship for the oxidation of organic contaminants by peracetic acid using GA-MLR method.

Peracetic acid (PAA) is considered as an effective and powerful oxidant for eliminating organic contaminants in wastewater treatment. The second-order rate constant (kapp) for the reaction of PAA with organic contaminants is practically important for evaluating their removal efficiency in wastewater treatment, but only limited numbers of kapp values are available. In this study, 70 organic compounds with various structures were selected, and the kapp of PAA with each organic compound was used to develop two quantitative structure-activity relationship (QSAR) models based on three kinds of descriptors including constitutional, quantum chemical, and the PaDEL descriptors. The genetic algorithm (GA) was applied to select the molecular descriptors, then the models developed by multiple linear regression (MLR). The most important descriptors that explain the reactivity of organic compounds with PAA are the EHOMO for the model with the constitutional and quantum chemical descriptors. The maxHdsCH and minHdCH2 are two most important descriptors for the model with only PaDEL descriptors. The developed models can be used to predict kapp for a wide range of organic contaminants. The accuracy of the developed models was proved by the internal, external validation and the Y-scrambling technique. The developed QSAR models using the GA-MLR method can be used as a screening tool for predicting the elimination of organic contaminants by PAA and increasing the understanding of chemical pollutant fate.

Potential anti-inflammatory effect of anti-HMGB1 in animal models of ICH by downregulating the TLR4 signaling pathway and regulating the inflammatory cytokines along with increasing HO1 and NRF2.

Intracerebral hemorrhage (ICH) is a severe clinical problem without effective treatment; the leading cause is neuroinflammation. High-mobility group box one protein (HMGB1) is an abundant protein in the cell nucleus of most mammalian cells, which exerts its function by binding to chromatin. The present study focused on the therapeutic effect of anti-HMGB1 on ICH via the downregulation of inflammatory pathways. The ICH mice models were created by collagenase IV injection in the striatum of mice. Then, mice were received different medications and divided into three groups: anti-HMGB1, anti-Toll-like receptor 4 (TLR4), and non-treated ICH groups. Cerebrospinal fluid (CSF) was obtained, and ELISA was carried out to determine the levels of inflammatory agents. Microglial cells were isolated from the cerebral hemispheres, and then Real-Time PCR and western blot were performed. The results showed that the anti-inflammatory effects of anti-HMGB1 were tremendous than anti-TLR4. Overall, the results showed that anti-HMGB1 had a more reducer effect on pro-inflammatory cytokines release (****P < 0.0001) and expression (****P < 0.0001) than anti-TLR4 when compared with the control group. It was also determined that anti-HMGB1 increased heme-oxygenase-1 (HO1) and nuclear factor erythroid-derived factor 2-related factor 2 (NRF2) (****P < 0.0001) expression in comparison with the control group while it was not significant for anti-TLR4 (CLI-095). The present study suggested that anti-HMGB1 serves as a potential anti-inflammatory molecule via reducing TLR4-related signaling pathways, pro-inflammatory cytokines production, and increasing the production of the anti-inflammatory cytokine along with heme-oxygenase-1 HO1 and NRF2 increment.

Catalyzed H2O2 decomposition over iron oxides and oxyhydroxides: Insights from oxygen production and organic degradation.

Iron minerals, such as iron oxides and iron oxyhydroxides, are the main influential soil components in catalyzed hydrogen peroxide propagation (CHP). Due to their dual effects on H2O2 activation to produce reactive oxygen species (ROS) and invalid consumption to produce oxygen, the intrinsic reactivity of iron minerals toward H2O2 decomposition requires comprehensive investigations. Herein, six iron minerals (hematite, magnetite, maghemite, goethite, feroxyhyte, and ferrihydrite) for H2O2 decomposition were investigated by a combination of normalized kinetic rate constants of H2O2 decomposition (NkH2O2), O2 production (NkO2), benzoic acid degradation (NkBA), and hexachloroethane degradation (NkHCA) over the surface area of each mineral. The results indicate H2O2 decomposition over iron minerals is a surface-related heterogeneous process. Hematite and goethite are the most promising minerals for environmental cleanup in terms of ROS production, because their H2O2 utilization efficiency for benzoic acid (BA) degradation (0.138 and 0.024 mol BA/mol H2O2 for hematite and goethite, respectively) are highest among the six iron minerals. Magnetite and maghemite are highly active for both H2O2 decomposition and O2 production at neutral and basic pHs. The presence of organic compounds suppresses O2 production by more than 60%, which favors H2O2 utilization. Ferrihydrite and feroxyhyte are considered as the problematic mineral for CHP due to that the two minerals acquire a high O2 production and negligible ROS generation at all pHs. The results of this study provide new insights to increase the understandings of H2O2-iron mineral systems and guide the application of iron minerals in chemical oxidation technologies.

Esophageal stenting in caustic injuries: a modified technique to avoid laparotomy.

OBJECTIVE: To compare the outcomes of a modified laparoscopic intraluminal stenting with the conventional laparatomic technique in patients with esophageal caustic injuries. METHODS: A total of 103 patients with esophageal burns were included in this retrospective analysis. Patients were candidates for esophageal stenting to prevent future stenosis. According to patient preference, stenting was done with either the innovatory stent with the modified technique (52 patients) or the conventional method that required laparotomy (51 patients). The modified technique consists of placing an inflation balloon stent via laparoscopy. Overall mortality and complications after follow-up period (3 months) were compared between the two groups. RESULTS: Two perioperative mortalities were seen, one in each group. Except one patient in the modified technique, all patients returned to normal intake after 3 months of follow-up. However, five patients of the modified group and three in the conventional group developed esophageal strictures (p > 0.05). Gastric outlet obstruction was observed in three patients of the modified group and one in the conventional group (p > 0.05). DeMeester scores showed that there was no gastro-esophageal reflux in both groups (p > 0.05). CONCLUSION: Our results show that the modified technique can reach the efficacy of the conventional method without requiring laparotomy. Thus, far several studies have demonstrated the advantages of laparoscopy over laparotomy. Thus, and in line with the clinical guidelines of the Society of American Gastrointestinal and Endoscopic Surgeons, we recommend using the presented modified technique in patients with caustic esophageal injuries.

The Effects of Air Pollution on Cardiovascular and Respiratory Causes of Emergency Admission.

INTRODUCTION: Today, air pollution is one of the critical problems in metropolitans and necessary preparations are needed for confronting this crisis. The present study was based on the goal of determining the relationship of air pollutant levels with the rate of emergency admissions for respiratory and cardiovascular patients. METHODS: In the present retrospective cross-sectional study, all respiratory and cardiovascular patients, referred to emergency department during 2012, were assessed. The meteorological and air pollution data were collected. Information regarding the numbers and dates (month, day) of admission for respiratory and cardiovascular diseases was achieved from the hospital's electronic registration system. The relation of air pollution and respiratory and cardiovascular admissions were analyzed by generalize additive model (GAM). RESULTS: 5922 patients were assessed which included 4048 (68.36%) cardiovascular and 1874 (31.64%) respiratory. Carbon monoxide (CO) level was an independent risk factor of cardiovascular disease on the same day (RR=1.49; 95% CI: 1.25- 1.77; P<0.001), the day before (RR=1.22; 95% CI: 1.02- 1.45; P=0.03), and the last two days (RR=1.3; 95% CI: 1.09- 1.54; P<0.001). The same process was repeated for ozone (O3). In addition, the O3 level on the same day (RR=1.49; 95% CI: 1.25- 1.77; P<0.001), the day before (RR=1.22; 95% CI: 1.02- 1.45; P=0.03), the last two days (RR=1.3; 95% CI: 1.09- 1.54; P<0.001), and the last week (RR=1.004; 95% CI: 1.0007-1.008; P=0.02) were independent risk factors of respiratory admissions. The increased level of particulate matter less than 2.5 micrometers in diameter (PM2.5) like O3 led to growth in the admissions to emergency department. CONCLUSION: The findings of the present study suggested that rising levels of CO and O3 during two days leads to a significant increase in cardiovascular admission on the third day. Furthermore, increase in O3, PM2.5, nitrogen dioxide (NO2), and CO levels causes a rise in respiratory admissions to emergency department.

Modified retro-tubercle opening-wedge versus conventional high tibial osteotomy.

Despite the fact that common surgical techniques for the treatment of genu varum usually correct the malalignment in the affected knee, these methods have significant complications and cause problems in the long term. Retro-tubercle opening-wedge high tibial osteotomy is among the newer techniques for the treatment of genu varum. The goal of this study was to compare the results of retro-tubercle opening-wedge high tibial osteotomy with those of medial opening-wedge osteotomy. In a randomized, controlled trial, 72 patients with varus knees who were scheduled for surgery were assigned into either the retro-tubercle opening-wedge high tibial osteotomy (n=34) or medial opening-wedge osteotomy groups (n=38). Groups were matched for age and sex. The position of the patella was compared with respect to the tuberosity and the upper tibial slope pre- and postoperatively. Patients were followed for an average of 13 months (range, 10-21 months). In the retro-tubercle opening-wedge high tibial osteotomy group, the length of the patellar tendon did not significantly differ pre- and postoperatively (P≥.5); however, in the medial opening-wedge osteotomy group, a statistically significant shortening was noted in patellar tendon postoperatively (P≤.05). Similarly, the tibial plateau inclination showed a statistically significant difference postoperatively in the medial opening-wedge osteotomy group, while the difference in the retro-tubercle opening-wedge high tibial osteotomy group did not reach statistical significance.