TEHRAN AIR POLLUTION MODELING USING LONG-SHORT TERM MEMORY ALGORITHM: AN UNCERTAINTY ANALYSIS

Air pollution is a major environmental issue in urban areas, and accurate forecasting of particles 10 μm or smaller (PM10) level is essential for smart public health policies and environmental management in Tehran, Iran. In this study, we evaluated the performance and uncertainty of long short-term memory (LSTM) model, along with two spatial interpolation methods including ordinary kriging (OK) and inverse distance weighting (IDW) for mapping the forecasted daily air pollution in Tehran. We used root mean square error (RMSE) and mean square error (MSE) to evaluate the prediction power of the LSTM model. In addition, prediction intervals (PIs), and Mean and standard deviation (STD) were employed to assess the uncertainty of the process. For this research, the air pollution data in 19 Tehran air pollution monitoring stations and temperature, humidity, wind speed and direction as influential factors were taken into account. The results showed that the OK had better RMSE and STD in the test (32.48 ± 9.8 μg/m3) and predicted data (56.6 ± 13.3 μg/m3) compared with those of the IDW in the test (47.7 ± 22.43 μg/m3) and predicted set (62.18 ± 26.1 μg/m3). However, in PIs, IDW ([0, 0.7] μg/m3) compared with the OK ([0, 0.5] μg/m3) had better performance. The LSTM model achieved in the predicted values an RMSE of 8.6 μg/m3 and a standard deviation of 9.8 μg/m3 and PIs between [2.7 ± 4.8, 14.9 ± 15] μg/m3

Identification of differential expressed transcripts of almond (Prunus dulcis ‘Sefied’) in response to water-deficit stress by cDNA-AFLP

Drought is the major abiotic stress with adverse effects on growth and productivity of plants. It induces the expression of various genes that are involved in stress response and tolerant/sensitive phenotypes. In this study, the expression of several genes were analyzed in response to dehydration in almond (Prunus dulcis 'Sefied') to shed light on the underlying genetic basis of water-deficit tolerance in almond. The advantages of using almond as a model system for studying dehydration tolerance in woody species are its small diploid genome and its adaptation to drought. Differential expression technique, cDNA-AFLP (amplified fragment length polymorphism), was used to find transcripts accumulated in young trees subjected to water-deficit treatment. Twenty transcript-derived fragments (TDFs) with differential expression between control and stress conditions were generated, amplified, and sequenced. The TDFs showing high homology with genes having known functions were validated by quantitative real-time PCR and their possible function(s) were discussed. These genes include: 2-deoxyglucose-6-phosphate phosphatase, protein kinase MK5 (AFC2) and urease, which up-regulated by 1.61, 2.39 and 4.87 fold under the water-deficit stress condition, respectively. In addition, network analysis unraveled a drought response mechanism displaying activation of the ABA signaling pathway via phosphorylation by 2-deoxyglucose-6-phosphate phosphatase and protein kinase MK5. Protein kinase MK5 was found to be a central element in the drought response network, displaying numerous interactions with RNA-splicing proteins, the sugar-mediated signaling pathway and an epigenetics response (histone phosphorylation).Maryam Shirani Bidabadi, Behrouz Shiran, Hossein Fallahi, Fariba Rafiei, Fazileh Esmaeili & Esmaeil Ebrahimi

Effects of low-intensity continuous ultrasound on hematological parameters of rats

Background: Low intensity ultrasound (US) has some well-known bio-effects which are of great importance to be considered. Objective: We conducted the present study to investigate the effects of low intensity continuous ultrasound on blood cells count in rat. Methods: Rats were anesthetized and blood samples were collected before US exposure. Then, they were exposed to US with nominal intensity of 0.2 W/cm2 at frequency of 3 MHz for a period of 10 minutes and this protocol was repeated for 7 days. Twenty four hours after the last US exposure, secondary blood samples were collected and the changes in blood parameters were evaluated. Results: Analysis revealed that platelets, hematocrit (HCT) and hemoglobin (HGB) were significantly different between experimental and sham groups but no difference between sham and control groups was observed. The results show that HCT and HGB of exposed rats were significantly reduced. Conclusion: This study shows that low intensity US may lead to side effects for hematological parameters such as reduction in the levels of HGB and HCT. © 2016 Shiraz University of Medical Sciences. All rights reserved

Investigation of itch in Parkinson disease

Introduction: Sensory abnormalities (eg, pain) are common in Parkinson disease (PD) with a negative impact on quality of life. As itch is less studied in PD, and pain and itch partially share sensory pathways, we designed this study to identify the occurrence and pattern of spontaneous itch, and responsiveness to a surrogate itch model in PD. Methods: The study protocol was approved (N-20180079) and PD patients and their best matched controls were recruited. A questionnaire was used to collect general information on itch. Sensory alterations were determined by subjective ratings and mechanical sensitivity threshold before and after a standard histamine-dependent itch model on forearms. Itch and pain intensities were rated on visual and numerical rating scales, respectively. Dispersion of itch was drawn on arm charts. Presence and area of alloknesis and hyperknesis were determined. Group comparisons were performed in SPSS with a significant level of 0.05. Descriptive statistic was used for questionnaire’s analysis. Results:Patients(n=20;68.10±7.91y,F/Mratio:8/12)andcontrols(n=20;67.35±7.65y,F/Mratio:8/12)wereexamined.PD patients rated less physical and emotional descriptors, except for the stinging (P = 0.028). No difference was found between the groups in histamine-provoked itch intensity (P = 0.799) or the itchy area. A significantly larger area of hyperknesis was found in PD (P = 0.011), but not for the area of alloknesis (P = 0.221). Sex-related responses yielded only a tendency toward higher responses in female patients. Discussion:PDdoesnotseemtoinfluenceperceptionofitch,neitherspontaneousnorevokeditch,exceptforhyperknesisarea,which was found significantly larger in PD patients following the application of histamine. This finding proposes a potential alteration in central processing of itch that needs further investigation and whether and how it is affected by, for example, PD pathogenesis

Use of sonic tomography to detect and quantify wood decay in living trees.

Premise of the studyField methodology and image analysis protocols using acoustic tomography were developed and evaluated as a tool to estimate the amount of internal decay and damage of living trees, with special attention to tropical rainforest trees with irregular trunk shapes.Methods and resultsLiving trunks of a diversity of tree species in tropical rainforests in the Republic of Panama were scanned using an Argus Electronic PiCUS 3 Sonic Tomograph and evaluated for the amount and patterns of internal decay. A protocol using ImageJ analysis software was used to quantify the proportions of intact and compromised wood. The protocols provide replicable estimates of internal decay and cavities for trees of varying shapes, wood density, and bark thickness.ConclusionsSonic tomography, coupled with image analysis, provides an efficient, noninvasive approach to evaluate decay patterns and structural integrity of even irregularly shaped living trees

An update on vitamin B12-related gene polymorphisms and B12 status.

Vitamin B12 is an essential micronutrient in humans needed for health maintenance. Deficiency of vitamin B12 has been linked to dietary, environmental and genetic factors. Evidence for the genetic basis of vitamin B12 status is poorly understood. However, advancements in genomic techniques have increased the knowledge-base of the genetics of vitamin B12 status. Based on the candidate gene and genome-wide association (GWA) studies, associations between genetic loci in several genes involved in vitamin B12 metabolism have been identified. The objective of this literature review was to identify and discuss reports of associations between single-nucleotide polymorphisms (SNPs) in vitamin B12 pathway genes and their influence on the circulating levels of vitamin B12. Relevant articles were obtained through a literature search on PubMed through to May 2017. An article was included if it examined an association of a SNP with serum or plasma vitamin B12 concentration. Beta coefficients and odds ratios were used to describe the strength of an association, and a  < 0.05 was considered as statistically significant. Two reviewers independently evaluated the eligibility for the inclusion criteria and extracted the data. From 23 studies which fulfilled the selection criteria, 16 studies identified SNPs that showed statistically significant associations with vitamin B12 concentrations. Fifty-nine vitamin B12-related gene polymorphisms associated with vitamin B12 status were identified in total, from the following populations: African American, Brazilian, Canadian, Chinese, Danish, English, European ancestry, Icelandic, Indian, Italian, Latino, Northern Irish, Portuguese and residents of the USA. Overall, the data analyzed suggests that ethnic-specific associations are involved in the genetic determination of vitamin B12 concentrations. However, despite recent success in genetic studies, the majority of identified genes that could explain variation in vitamin B12 concentrations were from Caucasian populations. Further research utilizing larger sample sizes of non-Caucasian populations is necessary in order to better understand these ethnic-specific associations

Removal of Hepatitis C Virus-Infected Cells by a Zymogenized Bacterial Toxin

Hepatitis C virus (HCV) infection is a major cause of chronic liver disease and has become a global health threat. No HCV vaccine is currently available and treatment with antiviral therapy is associated with adverse side effects. Moreover, there is no preventive therapy for recurrent hepatitis C post liver transplantation. The NS3 serine protease is necessary for HCV replication and represents a prime target for developing anti HCV therapies. Recently we described a therapeutic approach for eradication of HCV infected cells that is based on protein delivery of two NS3 protease-activatable recombinant toxins we named “zymoxins”. These toxins were inactivated by fusion to rationally designed inhibitory peptides via NS3-cleavable linkers. Once delivered to cells where NS3 protease is present, the inhibitory peptide is removed resulting in re-activation of cytotoxic activity. The zymoxins we described suffered from two limitations: they required high levels of protease for activation and had basal activities in the un-activated form that resulted in a narrow potential therapeutic window. Here, we present a solution that overcame the major limitations of the “first generation zymoxins” by converting MazF ribonuclease, the toxic component of the E. coli chromosomal MazEF toxin-antitoxin system, into an NS3-activated zymoxin that is introduced to cells by means of gene delivery. We constructed an expression cassette that encodes for a single polypeptide that incorporates both the toxin and a fragment of its potent natural antidote, MazE, linked via an NS3-cleavable linker. While covalently paired to its inhibitor, the ribonuclease is well tolerated when expressed in naïve, healthy cells. In contrast, activating proteolysis that is induced by even low levels of NS3, results in an eradication of NS3 expressing model cells and HCV infected cells. Zymoxins may thus become a valuable tool in eradicating cells infected by intracellular pathogens that express intracellular proteases

Detailed Analysis of a Contiguous 22-Mb Region of the Maize Genome

Most of our understanding of plant genome structure and evolution has come from the careful annotation of small (e.g., 100 kb) sequenced genomic regions or from automated annotation of complete genome sequences. Here, we sequenced and carefully annotated a contiguous 22 Mb region of maize chromosome 4 using an improved pseudomolecule for annotation. The sequence segment was comprehensively ordered, oriented, and confirmed using the maize optical map. Nearly 84% of the sequence is composed of transposable elements (TEs) that are mostly nested within each other, of which most families are low-copy. We identified 544 gene models using multiple levels of evidence, as well as five miRNA genes. Gene fragments, many captured by TEs, are prevalent within this region. Elimination of gene redundancy from a tetraploid maize ancestor that originated a few million years ago is responsible in this region for most disruptions of synteny with sorghum and rice. Consistent with other sub-genomic analyses in maize, small RNA mapping showed that many small RNAs match TEs and that most TEs match small RNAs. These results, performed on ∼1% of the maize genome, demonstrate the feasibility of refining the B73 RefGen_v1 genome assembly by incorporating optical map, high-resolution genetic map, and comparative genomic data sets. Such improvements, along with those of gene and repeat annotation, will serve to promote future functional genomic and phylogenomic research in maize and other grasses

A Single Molecule Scaffold for the Maize Genome

About 85% of the maize genome consists of highly repetitive sequences that are interspersed by low-copy, gene-coding sequences. The maize community has dealt with this genomic complexity by the construction of an integrated genetic and physical map (iMap), but this resource alone was not sufficient for ensuring the quality of the current sequence build. For this purpose, we constructed a genome-wide, high-resolution optical map of the maize inbred line B73 genome containing >91,000 restriction sites (averaging 1 site/∼23 kb) accrued from mapping genomic DNA molecules. Our optical map comprises 66 contigs, averaging 31.88 Mb in size and spanning 91.5% (2,103.93 Mb/∼2,300 Mb) of the maize genome. A new algorithm was created that considered both optical map and unfinished BAC sequence data for placing 60/66 (2,032.42 Mb) optical map contigs onto the maize iMap. The alignment of optical maps against numerous data sources yielded comprehensive results that proved revealing and productive. For example, gaps were uncovered and characterized within the iMap, the FPC (fingerprinted contigs) map, and the chromosome-wide pseudomolecules. Such alignments also suggested amended placements of FPC contigs on the maize genetic map and proactively guided the assembly of chromosome-wide pseudomolecules, especially within complex genomic regions. Lastly, we think that the full integration of B73 optical maps with the maize iMap would greatly facilitate maize sequence finishing efforts that would make it a valuable reference for comparative studies among cereals, or other maize inbred lines and cultivars