Miracle-dz/UniFAR-FTUs huggingface dataset:
Lipopolysaccharides and plant responses to phytopathogenic bacteria.

Abstract Treatment of the leaves of pepper (Capsicum annuum) cv. ECW10R with lipopolysaccharides (LPS) from both plant pathogenic and enteric bacteria alters several aspects of the plant response to subsequent inoculation with phytopathogenic xanthomonads. LPS pre-treatment prevents the hypersensitive reaction caused by strains of Xanthomonas campestris pv. vesicatoria carrying the avirulence gene avrBs1 (a gene-for-gene interaction) and by X. campestris pv. campestris (a non-host interaction). Associated with this effect are the earlier synthesis of feruloyl- and coumaroyl-tyramine, phenolic conjugates that are potentially antimicrobial, and alterations in the expression patterns of genes for some pathogenesis-related (PR) proteins. Similar effects on the timing of phenolic conjugate synthesis are also seen in the compatible interaction with X. campestris pv. vesicatoria, although the level of the response is lower. Recognition of LPS by plants may allow expression of resistance in the absence of catastrophic tissue damage. However phytopathogenic bacteria may have evolved mechanisms to suppress the effects of LPS (and of other non-specific bacterial elicitors) on plant cells.
Pedobacter bauzanensis sp. nov., isolated from soil.

A Gram-negative, aerobic, rod-shaped, non-motile bacterium, designated BZ42(T), was isolated from the soil of an industrial site. Strain BZ42(T) was able to grow at 5-25 °C. The major fatty acids were iso-C(15 : 0) (46.2 %), C(16 : 1)ω7c and/or iso-C(15 : 0) 2-OH (23.2 %) and iso-C(17 : 0) 3-OH (9.1 %). The predominant menaquinone was MK-7. The genomic DNA G+C content was 36.5 mol% (HPLC). 16S rRNA gene sequence phylogenetic analysis revealed that strain BZ42(T) was a member of the genus Pedobacter, family Sphingobacteriaceae, and 16S rRNA gene sequence similarities between strain BZ42(T) and the type strains of species of the genus Pedobacter with validly published names were 90.4-93.2 %. On the basis of phenotypic, chemotaxonomic and phylogenetic distinctiveness, strain BZ42(T) was considered to represent a novel species of the genus Pedobacter, for which the name Pedobacter bauzanensis sp. nov. is proposed. The type strain is BZ42(T) (=DSM 22554(T) =CGMCC 1.10187(T) =CIP 110134(T)).
Effect of percutaneous nephrolithotomy and tract dilatation methods on renal function: assessment by quantitative single-photon emission computed tomography of technetium-99m-dimercaptosuccinic acid uptake by the kidneys.

OBJECTIVES The aim of this study was to determine the impact of percutaneous nephrolithotomy (PCNL) and tract dilatation methods on global and regional renal function using quantitative single-photon emission computed tomography (QSPECT) of technetium-99m-dimercaptosuccinic acid ((99m)Tc-DMSA). METHODS Seventy-five patients undergoing PCNL between May 2008 and April 2009 were included in this randomized study. Of the 75 patients, 50 were evaluated by QSPECT of (99m)Tc-DMSA examinations before and at 3 to 6 months after surgery. This group of patients were categorized into three groups according to the dilatation technique used: group I (balloon dilator, n = 12 [24%] patients), group II (metal dilator, n = 14 [28%] patients), and group III (Amplatz dilator, n = 24 [48%] patients). RESULTS Of 50 renal units, new focal cortical defects on (99m)Tc-DMSA scan were seen in nine patients (18%). In six of these kidneys the site of focal defect corresponded to the access site for tract formation during PCNL (two in group II and four in group III). Total relative uptake and total area of treated kidney, for the entire group, increased from 42.2% and 42.3% preoperatively to 44.12% and 43.9% postoperatively. There was no statistically significant differences between the groups for total uptake and area of the treated kidneys before and after the procedure (p > 0.05 for each parameter). CONCLUSIONS QSPECT of (99m)Tc-DMSA confirms that renal function is preserved or often improved after percutaneous stone removal, and nephrostomy tract dilatation methods have similar effects on renal function.
Production of extracellular fructans by Gluconobacter nephelii P1464

Bacterial extracellular fructans, known as levans, have potential applications in food, pharmaceutical and cosmetic industries and high fructan producing strains could contribute into the cost reduction and more extensive commercial usage of them. An acetic acid bacteria (AAB) isolate P1464 was obtained from the Microbial Strain Collection of Institute of Microbiology and Biotechnology, University of Latvia and identified as Gluconobacter nephelii by DNA‐DNA hybridization and the formation of extracellular fructans by this strain was confirmed. Isolated extracellular fructose polymers were characterized using FT‐IR spectroscopy and the structural features of fructan appeared as similar to the reference sample of bacterial levan. Molecular mass estimates showed that the isolated G. nephelii P1464 fructose polymer has a relatively small molecular weight (Mw 1122·939 ± 153·453 kDa) and a sizeable polydispersity (Mw/Mn = 21·57 ± 1·60), as compared with other AAB, which could promote their physiological activity, including the prebiotic effects. Obtained at different cultivation conditions characteristics of fructan production, including the biotechnological indices such as the productivity (Qp) and yield (Yp/s) ranging from 0·774 to 1·244 g l−1 h and from 0·181 to 0·436 g g−1, respectively, confirmed, that G. nephelii P1464 could be used as promising strain for commercial production of levan.
Ultrasonography of the urinary tract in male sheep with urethral obstruction

PARTIAL or complete urethral obstruction is a common condition of intensively reared male lambs (entire and castrated) and mature rams. Early recognition of clinical signs by the farmer and prompt veterinary treatment are essential to ensure a satisfactory outcome because irreversible hydronephrosis quickly ensues from urinary back pressure. Early diagnosis is also important to allow rapid implementation of control measures to reduce the occurrence of future cases. As discussed in this article, ultrasonographic examination of the urinary tract can provide much useful information during the initial on-farm examination.
Spermine and L-Name Pretreatment Effects on Polyamine and Nitric Oxide Metabolism in Rat Brain During Seizures

Spermine and L-Name Pretreatment Effects on Polyamine and Nitric Oxide Metabolism in Rat Brain During Seizures In the CNS polyamines can exert opposite effects, depending on the concentration and conditions in the cell. Protective or neurotoxic polyamine effects were documented during seizures and repeated CNS excitation. Intensive research of exogenous polyamines effects during seizures induced by numerous agents did not clear up confusions about the duality of effects and the role of polyamines in seizures. In order to understand polyamine modulatory effects in seizures, the importance of NO and polyamine metabolism interdependence and the possible implication of changes of postulated NO and polyamine equillibrium in seizures, the effects of spermine alone and in combination with L-NAME (NOS inhibitor) on seizures induced by pentazol (PTZ) were investigated. To compare the obtained results, the effects of anticonvulsant midazolam on NO production during seizures were also investigated. Seizures were induced by i.p. application of pentazol (100 mg/kg b.w.). Spermine and L-NAME were administered i.p. before PTZ. In the striatum and hippocampus, spermine induced increased NO production (p<0.001) related to values in the group treated by PTZ. Application of L-NAME before spermine and PTZ caused decrease of NO production in comparison with animals treated only by PTZ or spermine and PTZ. L-NAME given before spermine exerts protective effects related to seizures induced by PTZ and to the group treated by spermine, extending the time of seizure symptoms appearance, thus confirming the NO signaling system involvement in spermine effects during seizures. Highly significant PAO activity increase caused by spermine points out the intensified interconversion of spermine into putrescine, in order to maintain the intracellular putrescine concentration. The obtained results prove a strong relationship between the NO signaling system and polyamine metabolism in the brain during seizures and the importance of their changes in this kind of CNS injury.
Yersinia pekkanenii sp. nov.

The taxonomic position of three strains from water, soil and lettuce samples was studied by using a polyphasic taxonomic approach. The strains were reported to lack the virulence-encoding genes inv and virF in a previous study. Controversially, API 20 E and some other phenotypic tests suggested that the strains belong to Yersinia pseudotuberculosis, which prompted this polyphasic taxonomic study. In both the phylogenetic analyses of four housekeeping genes (glnA, gyrB, recA and HSP60) and numerical analyses of HindIII and EcoRI ribopatterns, the strains formed a separate group within the genus Yersinia. Analysis of the 16S rRNA gene sequences showed that the strains were related to Yersinia aldovae and Yersinia mollaretii, but DNA-DNA hybridization analysis differentiated them from these species. Based on the results of the phylogenetic and DNA-DNA hybridization analyses, a novel species, Yersinia pekkanenii sp. nov., is proposed. The type strain is ÅYV7. 1KOH2(T) ( = DSM 22769(T) = LMG 25369(T)).
Detection of pathogenic Escherichia coli and microbiological quality of chilled shrimp sold in street markets

Foodborne illnesses caused by Escherichia coli are one of the most important gastrointestinal diseases and therefore represent a public health risk. The presence of E. coli in water or in products such as shrimp indicates faecal contamination. However, indicator micro‐organisms can be used to evaluate the microbiological quality of food sold in markets. This study focused on detecting isolates of E. coli containing the genes stx1A, stx2A, eae, LTI, STa, STb, aggR and pCVD432 in chilled shrimp sold in street markets in the municipality of São Paulo, Brazil, and to assess the microbiological quality of this product. Enteropathogenic and enterotoxigenic E. coli pathotypes were detected on the surface of two chilled shrimp samples. Salmonella spp. was not isolated. In addition, contamination of surface and muscle of the shrimp samples was found to be correlated. The detection of EPEC and ETEC pathotypes in chilled shrimp sold in street markets in Brazil provides useful epidemiological information for public health authorities to improve food safety and public health.
The postantibiotic effect and post‐β‐lactamase‐inhibitor effect of ceftazidime, ceftaroline and aztreonam in combination with avibactam against target Gram‐negative bacteria

The magnitudes of the postantibiotic effect (PAE) and post‐β‐lactamase‐inhibitory effect (PLIE) of ceftazidime‐avibactam, ceftaroline‐avibactam, and aztreonam‐avibactam were determined against isolates of Enterobacteriaceae and Pseudomonas aeruginosa that either harboured genes encoding serine and/or metallo‐β‐lactamases, or did not harbour bla genes. The bla genes included ones that encoded extended spectrum β‐lactamases, AmpC and KPC β‐lactamases, and one metallo‐β‐lactamase, NDM‐1. No substantial PAE was observed for any combination against any isolate. One substantial PLIE was found: a value of 1·9 h for ceftazidime‐avibactam against Klebsiella pneumoniae (blaKPC‐2). From comparison with results in the literature, we propose that the existence of a substantial PLIE depends on the bacterial isolate and on the specific β‐lactamase inhibitor and β‐lactam combination.
Detecting a novel Eriocheir sinensis reovirus by reverse transcription loop‐mediated isothermal amplification assay

The novel Eriocheir sinensis reovirus (EsRV) is a pathogen that causes severe disease and high mortality rates in cultivated crabs. Here, we established a highly sensitive and specific rapid reverse transcription loop‐mediated isothermal amplification (RT‐LAMP) assay that was cheaper and more suitable for field applications in crab aquaculture than those of traditional reverse transcription‐polymerase chain reaction (RT‐PCR) analysis. The amplification was completed within 45 min under isothermal conditions at 65°C. The RT‐LAMP test for EsRV had a detection limit of 15 pg, and sensitivity was 100 times greater than that of conventional RT‐PCR. The LAMP primers for EsRV were not amplified by other pathogen strains, indicating good specificity. In addition to detection by electrophoresis, RT‐LAMP results were detectable by visual observations of reaction tube turbidity, and calcein was added to visually detect the amplification products. These results indicate that this highly convenient, rapid and sensitive RT‐LAMP assay can be used to detect EsRV‐infected aquatic organisms.
Comparative assessment of a single surgeon's series of laparoscopic radical prostatectomy: conventional versus robot-assisted.

PURPOSE To directly compare the outcome of laparoscopic radical prostatectomy (LRP) with robot-assisted laparoscopic prostatectomy (RALP) performed by a single laparoscopic surgeon with intermediate experience-one who is between a novice and an expert. PATIENTS AND METHODS Consecutive 106 patients with prostate cancer who were treated with radical prostatectomy (62 with LRP and 44 with RALP) were included. The preoperative characteristics, the perioperative surgical outcomes, and the functional outcomes were compared between the two groups. RESULTS The mean operative time was longer in the RALP group (371 min vs 308 min, P = 0.00), conceivably because of more nerve-sparing procedures (84% vs 57%). The other perioperative parameters, including the surgical margin, were comparable, except for two major complications (rectourethral fistula and ureteral injury) in the LRP group. The RALP group recovered continence faster than those in the LRP, but the eventual continence rate at 12 months was similar (95% for LRP vs 94.4% for RALP, P = 1.00). The potency rate ≥ 6 months postsurgery was 47.6% in the LRP group and 54.5% in the RALP group (P = 0.65). CONCLUSIONS RALP was beneficial for the earlier recovery of continence, although LRP and RALP had comparable safety and efficacy as minimally invasive surgery for prostate cancer when performed by a laparoscopic surgeon with intermediate experience. Long-term follow-up data are needed for further evaluation of oncologic and functional outcomes for both techniques.
Impact of enumeration method on diversity of Escherichia coli genotypes isolated from surface water

There are numerous regulatory‐approved Escherichia coli enumeration methods, but it is not known whether differences in media composition and incubation conditions impact the diversity of E. coli populations detected by these methods. A study was conducted to determine if three standard water quality assessments, Colilert®, USEPA Method 1603, (modified mTEC) and USEPA Method 1604 (MI), detect different populations of E. coli. Samples were collected from six watersheds and analysed using the three enumeration approaches followed by E. coli isolation and genotyping. Results indicated that the three methods generally produced similar enumeration data across the sites, although there were some differences on a site‐by‐site basis. The Colilert® method consistently generated the least diverse collection of E. coli genotypes as compared to modified mTEC and MI, with those two methods being roughly equal to each other. Although the three media assessed in this study were designed to enumerate E. coli, the differences in the media composition, incubation temperature, and growth platform appear to have a strong selective influence on the populations of E. coli isolated. This study suggests that standardized methods of enumeration and isolation may be warranted if researchers intend to obtain individual E. coli isolates for further characterization.
Trend of extensively drug‐resistant Acinetobacter baumannii and the remaining therapeutic options: a multicenter study in Tehran, Iran over a 3‐year period

Comprehensive data on drug‐resistant patterns of Acinetobacter baumannii isolates in developing countries is limited. We conducted a multihospital study to assess the rate and trend of drug‐resistant phenotypes in Ac. baumannii using standardized definitions and to determine the remaining therapeutic options against resistant phenotypes. The 401 nonduplicate isolates were collected from six hospitals which are geographically distributed across Tehran, Iran over a 3‐year period. Following PCR of blaOXA‐51‐like gene, susceptibility testing was performed against nine antimicrobial agent categories. Three hundred and ninety (97%) isolates were resistant to least two carbapenems; carbapenem‐resistant Ac. baumannii. The majority of isolates (366, 91·3%) were extensively drug resistant (XDR) and the rest of the isolates were classified as multidrug resistant (26, 6·8%) and susceptible (9, 2·2%). The rate of XDR‐AB slightly decreased from 93·8% in 2011 to 89·8% in 2013. A considerable decrease in resistance to doxycycline, minocycline and tigecycline was demonstrated. The XDR‐AB isolates showed susceptibility to gentamicin (10·4%), tobramycin (23%), ampicilin–sulbactam (30·1%), minocycline (32·8%), tigecycline (10·7%), doxycycline (21·6%), colistin (100%) and polymixin B (100%). We demonstrated the rising trend of resistance to all antibiotic categories except tetracyclines and folate pathway inhibitors. We found that the treatment options against XDR‐AB are extremely limited and each treatment alternative including even old, but safe, antibiotics might be considered.
Factors influencing the utilisation of prevention of mother-to-child transmission (PMTCT) services by pregnant women in the Eastern Cape, South Africa

The aim of the study was to identify factors influencing the utilisation of Prevention of Mother-to-Child Transmission (PMTCT) in a resource poor setting in South Africa. Opsomming Die doel van die studie was om faktore te identifiseer wat die benutting van die Voorkoming van Moeder-tot-Kind Oordrag (VMTKO) beinvloed in ‘n omgewing in Suid-Afrika wat arm is aan hulpbronne. *Please note: This is a reduced version of the abstract. Please refer to PDF for full text.
Detection and molecular characterisation of Livestock-Associated MRSA in raw meat on retail sale in North West England

Limited data are available on the prevalence of livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) in the UK. We tested 124 raw meat samples for MRSA including pork (n=63), chicken (n=50) and turkey (n=11) collected from retail outlets in North West England between March and July 2015. MRSA was recovered from 9 (7.3%) samples (4 chicken, 3 pork, 2 turkey) from different butchers and supermarkets. Four were labelled of UK origin, 3 were from continental Europe; the origin was not specified for 2. Whole-genome sequencing (WGS), spa typing and the presence of lineage-specific canonical single nucleotide polymorphisms confirmed they belonged to the livestock-associated clade of clonal complex (CC) 398. Seven (77.8%) isolates were multi-drug resistant. Phylogenetic analyses showed the isolates were diverse, suggesting multiple silent introductions of LAMRSA into the UK food-chain. Two chicken meat isolates belonged to a sub-clade recently reported from human cases in Europe where poultry meat was the probable source. The low levels of MRSA identified (<20 CFU g) and absence of enterotoxin genes suggest the risk of acquisition of, or food-poisoning due to, LA-MRSA is low. Nevertheless, the MRSA contamination rate is higher than previously estimated; further evaluation of the public health impacts of LA-MRSA is warranted. A cc ep te d A rt ic le This article is protected by copyright. All rights reserved.
Phycicoccus cremeus sp. nov., isolated from forest soil, and emended description of the genus Phycicoccus.

A bacterial strain, designated V2M29(T), was isolated from forest soil collected in the Changbai Mountains, Heilongjiang Province, China. Cells of strain V2M29(T) were Gram-positive, rod-shaped (0.5-0.8 μm in diameter and 1.5-2.0 μm in length), strictly aerobic and non-motile. Colonies produced on R2A agar plates were creamy, smooth, circular and 0.3-0.8 mm in diameter. Strain V2M29(T) grew at 14-35 °C (optimum, 29 °C), at pH 4.1-10.0 (optimum, pH 7.0-8.0) and in the presence of 0-7.0 % (w/v) NaCl (optimum, 0-2.0 %). Strain V2M29(T) contained MK-8(H(4)) as the major respiratory quinone and iso-C(15 : 0) (20.9 %), iso-C(16 : 0) (18.5 %), C(17 : 1)ω8c (16.7 %) and 10-methyl-C(17 : 0) (9.2 %) as the major cellular fatty acids. The cell-wall peptidoglycan type was based on meso-2,6-diaminopimelic acid and the acyl type of the muramic acid was acetyl. Diphosphatidylglycerol, phosphatidylinositol and six unknown glycolipids were the major polar lipids. The G+C content of the DNA was 72.0 mol% (T(m)). 16S rRNA gene sequence analysis indicated that strain V2M29(T) was phylogenetically related to members of the genus Phycicoccus, with sequence similarities ranging from 96.6-97.8 %. The DNA-DNA relatedness values of strain V2M29(T) to Phycicoccus dokdonensis DS-8(T) and Phycicoccus bigeumensis DSM 19264(T) were 32.5±3.3 % and 29.2±2.3 %, respectively. Based on these results, it is concluded that strain V2M29(T) represents a novel species of the genus Phycicoccus, for which the name Phycicoccus cremeus sp. nov. is proposed, with V2M29(T) (=CGMCC 1.6963(T) =NBRC 104261(T)) as the type strain.
Oral supplementation of trans‐cinnamaldehyde reduces uropathogenic Escherichia coli colonization in a mouse model

Urinary tract infections (UTIs) in the United States result in more than 7 million hospital visits per year. Uropathogenic Escherichia coli (UPEC) is responsible for more than 80% of UTIs. Although antibiotics are the drug of choice to control UTIs, their repeated use has resulted in the emergence of antibiotic‐resistant UPEC. Thus, there is a need for effective alternate strategies to control UPEC infections. This study investigated the efficacy of trans‐cinnamaldehyde (TC), a food‐grade molecule present in cinnamon, in reducing UPEC colonization and pathogenesis in the lower UTI. Female C57BL/6 mice (6–8 weeks old) were fed ad libitum with 0, 0·1, 0·2 and 0·4% TC containing mouse chow for 10 days. Following TC supplementation, animals were experimentally infected with UPEC by transurethral catheterization. Mice were euthanized on days 1, 2 and 4 postinfection, and the bladder, urethra and urine were collected for bacterial enumeration. Prophylactic TC supplementation significantly (P ≤ 0·05) reduced UPEC colonization in the urinary bladder and urethra compared to the control. Results indicate that TC could potentially be used as an oral supplement to control UPEC‐associated lower UTIs, however, follow‐up clinical trials are warranted.