Complete genome sequences of three Prunus-infecting nepoviruses: apricot latent ringspot virus, myrobalan latent ringspot virus, and a novel virus from smooth stone peach (Prunus mira Koehne).

The complete genome sequences of two poorly studied Prunus-infecting nepoviruses, apricot latent ringspot virus (ALRSV) and myrobalan latent ringspot virus (MLRSV) were determined, confirming that they are members of subgroup C. Serological, biological, and molecular data, in particular a low level (58.8%) of amino acid sequence identity in the coat protein, suggest that ALRSV and MLRSV should be considered taxonomically distinct. In addition, data mining of public RNASeq data from wild and ornamental Prunus identified two contigs representing the nearly complete genome of a new subgroup A nepovirus from a smooth stone peach (Prunus mira) dataset (SRR8369794) from the Himalayas, for which the name "Prunus mira virus A" is proposed.

A Comparison Between Conventional and Terrain-Specific Adaptive Pushrim-Activated Power-Assisted Wheelchairs.

Pushrim-activated power-assisted wheels (PAPAWs) are assistive technologies that provide on-demand propulsion assistance to wheelchair users. In this study, we aimed to develop an adaptive PAPAW controller that responds effectively to changes in environmental conditions (e.g., type of surface or terrain). Experiments were conducted to collect kinematics of wheelchair motion using a frame-mounted inertial measurement unit (IMU) while performing a variety of wheelchair activities on different indoor/outdoor terrains. Statistical characteristics of velocity and acceleration measurements were extracted and used to develop a terrain classification framework to identify certain indoor and outdoor terrains. The terrain classification framework, based on random forest classification algorithms and kinematic features, was implemented and tested in our laboratory-developed PAPAW. This computationally efficient terrain classification framework was successfully implemented and tested in real-time. The power-assist ratio of each wheel was adjusted based on the type of terrain (e.g., more assistance was provided on outdoor terrains). Our findings revealed that propulsion effort (e.g., peak input torque) on asphalt was significantly reduced when using adaptive controllers compared to conventional PAPAW controllers. In addition, subjective views of participants regarding the workload of wheelchair propulsion (e.g., physical/cognitive effort) supported the positive effects of adaptive PAPAW controllers. We believe that the adoption of terrain-specific adaptive controllers has the potential to improve the accessibility of outdoor terrains and to prevent or delay upper extremity joint degeneration or pain.

A Comparison Between Conventional and User-Intention-Based Adaptive Pushrim-Activated Power-Assisted Wheelchairs.

Pushrim-activated power-assisted wheel (PAPAW) users ideally require different levels of assistance depending on activity and preference. Therefore, it is important to design and develop adaptive PAPAW controllers to account for these differences. The main objective of this work was to integrate a user intention estimation framework into a PAPAW and develop personalized adaptive controllers. We performed experiments to gather kinetics of wheelchair propulsion for a variety of daily life wheelchair activities. The propulsion characteristics (i.e., pushrim forces) were used to train intention estimation models and characterize implicit user intentions when performing daily life wheelchair maneuvers. These intentions included moving straight forward, performing a right/left turn, and braking. The intention estimation framework, based on random forest classification algorithms and kinetic features, was implemented and tested in our laboratory-developed PAPAW. This computationally efficient framework was successfully implemented and tested for each participant in real-time. Our results revealed that the real-time user intention predictions were similar to the offline models. The power-assist ratio of each wheel was adjusted based on which user intention was identified. Data collected from four participants provided evidence regarding the effectiveness of using adaptive intention-based controllers. For instance, the propulsion effort was significantly reduced when using an adaptive PAPAW controller. Subjective views of participants regarding the workload of wheelchair propulsion (e.g., physical/cognitive effort) were also gathered. Our findings suggest that rankings of different controllers varied among different participants and across different wheelchair maneuvers, indicating the need for customized adaptive controllers to fit different users' activities and preferences.

Does the BCG vaccine have different effects on strains of tuberculosis?

Several explanations have been suggested concerning the variety in bacille Calmette-Guerin (BCG) vaccine efficacy on strains of Mycobacterium tuberculosis (Mtb). This study aimed to compare the effect of BCG vaccination history in the prevention of the occurrence of Mtb-Beijing and non-Beijing strains. In this cross-sectional study, 64 patients with pulmonary tuberculosis (TB) were recruited from the Iranian border provinces (North West and West). Isolates were subjected to restriction fragment length polymorphism (RFLP) analysis, using the insertion sequence IS6110 as a probe (IS6110 RFLP) and drug susceptibility testing using the proportion method. Samples were analyzed with Gel Compare II 6.6 and spss version 18. The mean age [standard deviation (SD)] of the patients was 54·4 (SD = 17·0). Overall, 49 cases (76·56%) had no BCG vaccination scar. The prevalence of Beijing strains was 9·38% and drug resistance proportion among the isolates was 14·1% (nine cases). There was a significant relationship between Beijing strains and tuberculosis (TB)-drug resistance in isolates (χ2  = 26·29, P < 0·001). There was also a strong association between vaccination history and Beijing strains (χ2  = 13·23, P = 0·002). Also, a statistical relationship was observed between Beijing strains and drug-resistant TB among patients with a history of vaccination (χ2  = 7·47, P = 0·002). This association was not maintained in the unvaccinated group (P = 0·102). These findings confirm the claim that the vaccine has different effects on different subspecies of tuberculosis. The cause of the high probability of drug resistance in patients with Beijing-TB and vaccination history requires further investigation with a higher sample size.

Molecular detection of Coxiella burnetii in horse sera in Iran.

Coxiella burnetii is a zoonotic bacterium that can infect a wide range of animals including horses. However, its circulation dynamics in and through horses are still unclear. The aim of this study was to evaluate prevalence of C. burnetii and its genomic characteristics in horse sera samples in the North of Iran (Golestan Province). The samples were collected in 2018 and the age, sex, and breed of each animal were recorded. Nested-PCR was used to detect C. burnetii based on the presence of the transposable gene IS1111. The results showed that 7.50 % (P < 0.05; 95 % CI: 0.5 %-0.12 %) of the examined sera samples were positive for C. burnetii. Based on the resuls, prevalence of C. burnetii in the age groupof < Years 1-5 (p-value <0.05, 95 % CI: 1 %-8 %) was less than the age group of >6 years old (p-value <0.05, 95 %, CI: 7 %-19.8 %). In previous studies, it was concluded that the horses' population in Golestan Province should be considered as an important factor in the epidemiology of Q fever and consequently in public health. Further studies should be implemented to evaluate if horses may be relevant indicators of zoonotic risk in urban and suburban endemic areas.

Prevalence of C. burnetii DNA in sheep and goats milk in the northwest of Iran.

Q fever is a common zoonotic disease with worldwide distribution. The causative agent of Q fever is Coxiella burnetii, a gram-negative and polymorphic rod bacterium. Sheep and goats are the primary reservoirs of this disease, although a variety of animal species can be infected. The main route of Q fever transmission from animals to humans is the inhalation of contaminated aerosols with C. burnetii. The bacterium is excreted in milk of infected animals and therefore; the consumption of unpasteurized milk and dairy products might be a route of coxiella burnetii transmission from animals to humans. The present study was conducted to determine the prevalence of C. burnetii in milk samples collected from sheep and goats in west Azerbaijan province, Iran. During 2018, a total number of 420 milk samples were collected from sheep (n = 210) and goats (n = 210) of different regions of the province. All milk samples were subjected to DNA extraction and examined by a highly and specific nested-PCR method. The results showed that 51 (12.1%) (95% CI: 9.3%-15.6%) examined samples [sheep; n = 16 (7.6%) and goat; n = 35 (16.6%)] were positive for C. burnetii. The prevalence of C. burnetii in goat milk samples was significantly higher than sheep milk samples (P < 0.05). The shedding of C. burnetii in milk was significantly higher in summer (25%) (P < 0.05, 95% CI: 17.7%-34%) than the other seasons. It was concluded that sheep and goat populations in west Azerbaijan play an important role in the epidemiology of Q fever.

Comparing IS6110-RFLP, PGRS-RFLP and IS6110-Mtb1/Mtb2 PCR methods for genotyping of Mycobacterium tuberculosis isolates.

AIMS: Tuberculosis (TB) is still an important disease in the world, especially in developing countries. Applying efficient and suitable methods for genotyping Mycobacterium tuberculosis (MTB) isolates is a crucial step for identifying the MTB transmission mode and controlling its subsequent outcomes. Considering the complexity of IS6110-RFLP and PGRS-RFLP methods for MTB classification, suggesting other simple but reliable techniques could be helpful in the MTB studies, especially in low-income countries. METHODS AND RESULTS: This study aimed to evaluate the capabilities of three methods for genotyping MTB isolates collected from Iran through comparing our previously published results for IS6110-RFLP and PGRS-RFLP methods and current results obtained from IS6110-Mtb1/Mtb2 PCR technique. A strong concordance was observed between the results of clustering by three techniques. Calculated Kendall's Tau concordance value for correlation of IS6110-RFLP and IS6110-Mtb1/Mtb2 PCR, for IS6110-RFLP and PGRS-RFLP, and for IS6110-Mtb1/Mtb2 PCR and PGRS-RFLP techniques was equal to 0·943, 0·898 and 0·85 respectively. CONCLUSIONS: A strong correlation between IS6110-Mtb1/Mtb2 PCR, and IS6110-RFLP and PGRS-RFLP methods was observed and therefore IS6110-Mtb1/Mtb2 PCR discriminates MTBs capably. SIGNIFICANCE AND IMPACT OF THE STUDY: The study showed that IS6110-Mtb1/Mtb2 PCR, which is a simple and economical MTB genotyping approach, could be a more appropriate method to be applied in the low-budget research programmes.

Is there any correlation between sperm parameters and chromatin quality with embryo morphokinetics in patients with male infertility?

The main goal was to evaluate the correlation between sperm parameters and chromatin quality with embryo kinetics via time-lapse monitoring system (TLM). A total of 40 couples involved in the ICSI program as a result of male infertility. For assessment of sperm chromatin and DNA quality, we used aniline blue, toluidine blue, chromomycin A3, acridine orange and terminal transferase-mediated deoxyuridine triphosphate biotin end labelling assays. All mature oocytes were injected, and the generated zygotes (2PNs) were cultured in TLM. In day 3 after injection, single embryo transfer (SET) was carried out according to the morphology and morphokinetics. The patients were followed up until delivery. There were positive significant correlations between sperm count with CC2 (r = .330, p = .049), T4 (r = .329, p = .038), T6 (r = .342, p = .035) and T7 (r = .374, p = .025). Also, there were positive significant correlations between nonprogressive motility and T2 (r = 0.323, p = .042), T3 (r = .411, p = .013) and T4 (r = .418, p = .007). Regarding the sperm chromatin quality assays, there were negative significant correlations between CMA3 and CC2 (r = -.272, p = .049) and between acridine orange and T5 (r = -.221, p = .040). It seems that the abnormal sperm parameters and chromatin alteration affect the normal embryo kinetics in ICSI program.

Sperm chromatin quality and DNA integrity in partial versus total globozoospermia.

Globozoospermia is a severe form of teratozoospermia with low incidence in infertile patients, considered as one of the important causes of male infertility. The objective was to investigate the chromatin/DNA integrity as well as apoptosis in ejaculated spermatozoa of cases with partial or total globozoospermia. Fifty-seven semen samples were divided into three groups of partial globozoospermia (n = 17), total globozoospermia (n = 10) and normozoospermia (control; n = 30). Sperm chromatin condensation, DNA integrity and apoptosis were assessed using cytochemical assays. The results showed significant differences in sperm parameters of count and motility between two case groups versus controls. The percentages of spermatozoa with abnormal chromatin packaging and protamine deficiency were significantly higher in total and partial globozoospermic men compared to normozoospermic samples. Also, the rates of TUNEL-positive spermatozoa were significantly increased in both globozoospermic cases with respect to the control (18.3 ± 10.1 and 12.3 ± 9.2 versus 5.9 ± 3 respectively). However, no significant differences were noticed between two subgroups of patients with regard to sperm DNA denaturation, DNA fragmentation and apoptosis. Abnormal chromatin packaging, DNA damage and apoptosis were significantly higher in cases than controls. The sperm chromatin/DNA anomalies may be considered as one of the main aetiology of ART failure in globozoospermic patients.

Isolation and biotyping of Brucella spp. from sheep and goats raw milk in southeastern Iran.

Brucellosis is known as an important public health problem for humans around the world and is one of the most prevalent zoonotic disease as well. Brucella spp. is a Gram negative rod, facultative intracellular pathogenic and non motile bacteria. The aim of this study were to determine the frequency and biotyping of Brucella spp. isolated from sheep and goats from south eastern part of Iran. 700 samples (raw milk) from sheep and goats (90) flocks were collected randomly, from January to July 2015, samples were transferred packed in ice to microbiology lab in Kerman University, immediately. Samples were inoculated on Brucella agar which contains antibiotic and inactivated horse serum and incubate for 5 days. Gram smears were prepared from suspected colonies followed by oxidize and biochemical tests. Polymerase Chain Reaction (PCR) were used for confirmation. All positive samples were biotyped by phage typing. Nine milk samples out of 700 (1.28%) collected were positive by bacteriological method and all of them were Brucella melitensis Biotype 1 and one out of 700 samples was Brucella ovis. In relation to the National vaccination program in these areas the most contaminated region was Rabor, Rayen, Bardsir and Baft, respectively.

Cryoprotectant-free vitrification of human spermatozoa in new artificial seminal fluid.

Vitrification is a new method that has been recently introduced in Assisted Reproduction Technique programs. The aim of this study was to design a new medium similar to normal human seminal fluid (SF), formulation artificial seminal fluid (ASF), and to compare the cryoprotective potency of this medium with SF and human tubal fluid (HTF) medium. Thirty normal ejaculates were processed with the swim-up technique and sperm suspensions were divided into four aliquots: (i) fresh sample (control); (ii) vitrification in HTF medium supplemented with 5 mg/mL human serum albumin and 0.25 mol sucrose (Vit HTF); (iii) vitrification with patients' SF (Vit SF); and (iv) vitrification in ASF (Vit ASF). After warming, sperm parameters of motility, viability, and morphology were analyzed using WHO criteria. Also, sperm pellets were fixed in 2.5% glutaraldehyde and processed for scanning electron microscopy and transmission electron microscopy observations. The results showed that progressive motility (46.09 ± 10.33 vs. 36.80 ± 13.75), grade A motility (36.59 ± 11.40 vs. 16.41 ± 11.24), and normal morphology (18.74 ± 8.35 vs. 11.85 ± 5.84) and viability (68.22 ± 10.83 vs. 60.86 ± 11.72) of spermatozoa were significantly higher in Vit ASF than in Vit HTF. All parameters were better in Vit ASF than in Vit SF, but only viability was significantly different (p = 0.006). After cryopreservation, deep invagination in cytoplasm and mechanically weak point sites and folded tail were commonly observed. But, this phenomenon was more significant in Vit HTF and Vit SF than in ASF (p < 0.05). In transmission electron microscopy evaluation, acrosome damage, plasma membrane loss, chromatin vacuolation, and disruption of mitochondria arrangement and structures were observed in all vitrified groups. Adherence of several tail sections together was also seen in all cryo groups. But this was seen more in Vit HTF and Vit SF than in ASF (p < 0.05). In conclusion, vitrification of human spermatozoa with ASF can effectively preserve the quality of sperm motility in comparison with Vit HTF.

Higher circulating levels of chemokines CXCL10, CCL20 and CCL22 in patients with ischemic heart disease.

Recruitment of leukocytes is one of the earliest events in the pathogenesis of ischemic heart disease (IHD) and chemokines play an important role in the migration of these cells into the inflammation sites. The aim of this study was to evaluate the CXCL10, CCL20 and CCL22 levels and the single nucleotide polymorphisms (SNPs) rs4508917, rs6749704 and rs4359426 in chemokine genes in patients with IHD to clarify any association. A total of 300 patients with IHD as having acute myocardial infarction (AMI; n=100), stable angina (SA; n=100) or unstable angina (UA; n=100) and 100 healthy subjects as a control group were enrolled to study. Serum samples from all participants were tested for the CXCL10, CCL20 and CCL22 levels by using ELISA. The SNPs were determined by polymerase chain reaction-restriction length polymorphism (PCR-RFLP) method. The mean serum concentrations of CXCL10, CCL20 and CCL22 in AMI patients (395.97±21.20Pg/mL, 108.38±10.31Pg/mL and 1852.58±205.77Pg/mL), SA patients (405.48±27.36Pg/mL, 90.20±7.69Pg/mL and 2322.04±231.23Pg/mL) and UA patients (396.69±22.79Pg/mL, 141.87±18.10Pg/mL and 2754.89±211.70Pg/mL) were significantly higher than in the healthy group (179.38±8.85Pg/mL, 51.92±4.62Pg/mL and 451.82±23.76Pg/mL, respectively; P<0.001). Similarly, the serum levels of CXCL10, CCL20 and CCL22 in total IHD patients (399.38±13.77Pg/mL, 113.49±7.48Pg/mL and 2309.84±126.39Pg/mL, respectively) were also significantly higher as compared with healthy subjects (P<0.001). The serum levels of CCL20 and CCL22 in UA patients were significantly higher than those in SA and AMI patients, respectively (P<0.01 and P<0.003, respectively). The serum levels of CXCL10 and CCL20 in diabetic patients were significantly higher in comparison to non-diabetic patients (P<0.05 and P<0.02, respectively). The serum levels of CCL22 in dyslipidemic- and obese patients were also significantly higher in comparison with non-dyslipidemic- and non-obese patients, correspondingly (P<0.05 and P<0.01, respectively). There were no significant differences between men and women or between patients who treated with statin, aspirin, ß-blockers or angiotensin converting enzyme (ACE) inhibitors and patients without mentioned treatment regarding the levels of chemokines. The frequency of the GG genotype at SNP rs4508917 in CXCL10 gene was higher, whereas the frequency of the AA genotype at SNP rs4359426 in CCL22 gene was lower in total patients with IHD as compared with healthy subjects (P<0.04 and P<0.002, respectively). These results showed that the higher levels of CXCL10, CCL20 and CCL22 were associated with IHD. The serum levels of chemokines may influence by the certain traditional risk factors of IHD and some studied SNPs, but did not influence by treatment and gender of patients.

Impact of gender and menopausal status on metabolic parameters in chronic hepatitis C infection.

Hepatitis C infection (HCV) and menopause are associated with insulin resistance (IR), and IR accelerates HCV-induced liver disease. The relationship between menopause and IR has not been studied in this population. This study aimed to assess the impact of menopause on IR and metabolic syndrome in HCV. One hundred and three (69 men, 16 premenopausal, 18 postmenopausal women) noncirrhotic, nondiabetic HCV-infected adults underwent IR measurement via steady-state plasma glucose during a 240-min insulin suppression test. Metabolic syndrome was defined by at least three of five standard laboratory/clinical criteria. The patient characteristics were as follows: mean age 48 years, waist circumference 94.4 ± 12.4 cm and 37.9% Caucasian. SSPG was higher in postmenopausal than premenopausal women or men (mean difference 18, 95% CI -41 to 76 and 35, 95% CI -3 to 72 mg/dL; respectively). After adjusting for waist circumference, female gender, nonwhite race and triglycerides were positively associated and high-density lipoprotein negatively associated with steady-state plasma glucose. Compared to men, both pre- (Coef 48, 95% CI 12-84) and postmenopausal women (Coef 49, 95% CI 17-82) had higher steady-state plasma glucose. Compared to premenopausal women, men (OR 2.0, 95% CI 0.38-10.2) and postmenopausal women (OR 2.9, 95% CI 0.46-18.8) had higher odds of metabolic syndrome, but this was statistically nonsignificant. Both liver inflammation (OR 7.9) and nonwhite race (OR 6.9) were associated with metabolic syndrome. We conclude that women are at inc-reased risk for IR in HCV. There may also be an increased risk of metabolic syndrome postmenopause. Along with lifestyle modification and weight loss, women with metabolic abnormalities represent an especially at-risk group warranting HCV treatment to prevent adverse metabolic outcomes.

The Effects of Solvent Polarity on Hypoglycemic and Hypolipidemic Activities of Securigera Securidaca (L.) Seeds.

The search for indigenous natural antidiabetic and antilipidemec agents is still ongoing. Medicinal plants are widely used for this purpose. These herbs are very rich sources of bioactive compounds as flavonoids, polyphenols, tannins, alkaloids which have been reported as effective role to reduce blood glucose and lipid levels. Securigera securidaca seed is reputed in folk medicine for their value as antidiabetic and antilipidemec drugs. In this research, the effect of solvent polarity in bioactive extraction contents of this plant was evaluated by GC-MS analysis. Then antidiabetic and antilipidemic activies of different extracts were investigated in streptozotocine-induced diabetic rats and compared to glibenclamide as known chemical drug for diabetes.The results indicated that, carbon tetrachloride extract of Securigera securidaca seeds showed the best and significant hypoglycemic and hypolipidemic activities compared to other extracts because of its more sterols and fatty acids content with beta cells protecting effect from high glucose-induced apoptosis and also increasing in insulin level and sensitivity.

Tick diversity and detection of Coxiella burnetii in tick of small ruminants using nested Trans PCR in Southeast Iran.

Ticks are obligatory bloodsucking arthropods, and probably the most harmful ectoparasites that may cause some tick born diseases. The main objective of this study was to determine the prevalence, diversity and seasonal distribution of ticks and using a nested Trans PCR to identify Coxiella burnetii in ticks collected from small ruminants in Sistan and Balouchestan province, southeast Iran. A total 1305 ticks were collected from 272 Sheep and 253 Goats during May 2014 to April 2015. Prevalence of ixodid tick infestation in small ruminants was 58.4%. Of all examined ticks, nine tick species were identified as follow: Hyalomma anatolicum anatolicum (30.3%), Rhipicephalus sanguineus (21%), Hyalomma anatolicum excavatum (19%), Rhipicephalus turanicus (9%), Rhipicephalus bursa (6.7%), Hyalomma detritum (4.7%), Hyalomma dromedarii (4.4%), Hyalomma asiaticum asiaticum (4.4%) and Hyalomma marginatum (0.5%). The nested Trans PCR examination of ixodid ticks revealed that Hyalomma anatolicum anatolicum and Rhipicephalus sanguineus were infected with C. burnetii. The results of the present study revealed that ixodid ticks infestation was widespread and shows their role as putative vectors and reservoirs for this pathogenic agent in southeast Iran. Hence; Q fever should be considered a significant public health threat in this region.

Molecular Epidemiology of Mycobacterium Tuberculosis Strains in the North-West and West of Iran.

BACKGROUND: Identifying Mycobacterium tuberculosis (MTB) transmission type is a key step in the control of this disease. AIM: This study aimed to determine the path and transmission type of MTB and the insertion sequence IS6110 band number and verify their relationship to demographic and clinical risk factors. SUBJECTS AND METHODS: In this cross-sectional study, 64 MTB patients from three border provinces of Iran were selected after full clinical history and physical evaluation design. The drug susceptibility testing was carried out using the standard proportion technique on sputum samples. Isolates tested with restriction fragment length polymorphism technique used IS6110. RESULTS: Recent transmission of disease was 33/50 (66%) based on clustering rate. The IS6110 band number had a significant relationship with drug resistance detected in proportion method tested by univariate linear regression (P < 0.01). Furthermore, the IS6110 band number had association with Bacillus Calmette-Guérin vaccination history (P = 0.02), sex (P < 0.01), and purified protein derivative (PPD) reaction size (P < 0.01) tested by multiple analysis. The risk of recent transmission inferred from the clustering rate was significantly higher in patients from Western provinces compared to those from the North-West province (P = 0.048). However, age (P = 0.39), gender (P = 0.16), vaccination history (P = 0.57), drug susceptibility, and PPD (P < 0.6) were independent of clustering. The largest cluster of up to six subjects was found in the Western provinces. CONCLUSION: Recent MTB transmission was much more common in the West compared to the North-West of Iran. Large MTB clusters with strong epidemiological links may be reflective of a disease outbreak. Correlation noted between the IS6110 band number and vaccination history; PPD size and female gender necessitates further studies.