Miracle-dz/UniFAR-FTUs huggingface dataset:
Skatole remediation potential of Rhodopseudomonas palustris WKU‐KDNS3 isolated from an animal waste lagoon

Skatole (3MI) is a major contributor to the malodor emission resulting from ruminant and human faeces. The remediation of malodor has been a major challenge for the animal production industry. In this investigation, a pure culture of purple nonsulphur bacterium capable of degrading 3MI was isolated from a swine waste lagoon using an enrichment technique and identified as Rhodopseudomonas palustris WKU‐KDNS3 based on 16S rRNA analysis and UV‐visible spectroscopy. The cell structure of the organism was confirmed by transmission electron microscopy. Growth profile and 3MI removal pattern were determined using media supplemented with 0·1 μmol 3MI under short‐term and long‐term aerobic growth conditions. The organism grew on 3MI media as luxuriantly as control (without 3MI). Growth of R. palustris WKU‐KDNS3 demonstrated a significant reduction in the level of 3MI (>48%) in 72 h. The level of 3MI dropped further by >93% of the total concentration present in the medium in 21 days. Skatole remediation potential of R. palustris WKU‐KDNS3 can be judiciously utilized in various animal and industrial waste treatment systems.
Phylogenetic diversity of sulphate‐reducing Desulfovibrio associated with three South China Sea sponges

Marine sponges harbour dense and diverse micro‐organisms which includes sulphate‐reducing bacteria (SRB). SRB are known to play a key role in the cycling of marine elements. However, in contrast to carbon and nitrogen cycling bacteria, SRB associated with marine sponges are largely unexplored. In this study, we explored the phylogenetic diversity of the SRB associated with three shallow‐water sponges Arenosclera heroni, Dysidea arenaria and Astrosclera willeyana from the South China Sea by cloning‐and‐sequencing approach of SRB 16S rRNA gene with specific primers. The results showed that SRB associated with sponges mainly belonged to the genus Desulfovibrio in the class Deltaproteobacteria, i.e. a total of 14 Desulfovibrio‐related OTUs were obtained from three sponges. The exception is identical OTUs from different sponges. Each sponge species harboured a unique set of Desulfovibrio OTUs, with only a few shared OTUs observed between species, suggesting different species of Desulfovibrio in different species of sponges. Meanwhile, some Desulfovibrio OTUs had a low similarity (<97%) with related sequences in GenBank and phylogenetic analysis indicating novel Desulfovibrio symbionts in sponges. The results contribute to the overall understanding of the phylogenetic diversity of SRB associated with sponges.
Diagnosis of bovine tuberculosis using a metal oxide‐based electronic nose

Electronic noses (e‐noses) have been used for environmental monitoring, standardization of medicinal flavourings, food safety tests and diagnosis of infectious diseases based on the statistical analysis of volatile organic compounds (VOCs). Bovine tuberculosis (bTB) is officially diagnosed using the intradermal skin test (IST), which is time‐consuming and labour‐intensive. Therefore, a more convenient and rapid test with greater sensitivity would be advantageous as prescreening test. In this study, we used a metal oxide sensor (MOS) type e‐nose to analyse VOCs in a bTB‐infected (n = 11) and bTB‐free (n = 10) sera, from cattle whose health status was confirmed using the IST, and pathological and bacteriological examinations. The differences in VOCs from bTB‐infected and bTB‐free sera detected by the e‐nose were statistically analysed using principal components and discriminant factor analyses. bTB‐infected and bTB‐free sera could be discriminated by MOS type e‐nose, and analysing time per sample was only 20 min. VOC analysis using a MOS e‐nose was a rapid and automated prescreening method to diagnose bTB, and can be used to select bTB‐suspect cattle for IST confirmation. Further studies are required to estimate test sensitivity and specificity.
A novel hydroxamic acid‐containing antibiotic produced by a Saharan soil‐living Streptomyces strain

During screening for potentially antimicrobial actinobacteria, a highly antagonistic strain, designated WAB9, was isolated from a Saharan soil of Algeria. A polyphasic approach characterized the strain taxonomically as a member of the genus Streptomyces. The strain WAB9 exhibited a broad spectrum of antimicrobial activity toward various multidrug‐resistant micro‐organisms. A PCR‐based assay of genomic potential for producing bioactive metabolites revealed the presence of PKS‐II gene. After 6 days of strain fermentation, one bioactive compound was extracted from the remaining aqueous phase and then purified by HPLC. The chemical structure of the compound was determined by spectroscopic (UV–visible, and 1H and 13C NMR) and spectrometric analysis. The compound was identified to be 2‐amino‐N‐(2‐amino‐3‐phenylpropanoyl)‐N‐hydroxy‐3‐phenylpropanamide, a novel hydroxamic acid‐containing molecule. The pure molecule showed appreciable minimum inhibitory concentration values against a selection of drug‐resistant bacteria, filamentous fungi and yeasts.
Characterization of Listeria monocytogenes from three countries and antibiotic resistance differences among countries and Listeria monocytogenes serogroups

A total of 104 Listeria monocytogenes isolates from 330 fish samples from three countries were characterized by multiplex PCR for serogrouping and virulence markers determination and tested for antibiotics resistance. A 53·8% of the isolates belonged to serogroup 1/2a, 3a; 32% belonged to 1/2b, 3b, 7; 14·4% belonged to 4b, 4d, 4e and 1% belonged to 1/2c, 3c. All isolates exhibited resistance to at least one antibiotic but the resistance rates varied among countries. The isolates exhibited high resistance to penicillin, rifampicin, clindamycin, erythromycin and tetracycline, but low resistance to amoxicillin‐clavulanic acid, streptomycin, sulfamethoxazole–trimethoprim, gentamicin, chloramphenicol and kanamycin. When comparing countries, the resistance rate for rifampicin, clindamycin, erythromycin, tetracycline, amoxicillin‐clavulanic acid varied among countries. When comparing serogroup, 1/2a, 3a exhibited the highest resistance to clindamycin, erythromycin, tetracycline and vancomycin while serogroup 4b, 4d, 4e exhibited the highest resistance to amoxicillin‐clavulanic acid. All isolates carried inlA, inlC, inlJ and lmo2672. Listeriolysin S was carried by 42 and 30% of 4b and 1/2b isolates respectively.
Brome mosaic virus, good for an RNA virologist's basic needs.

Abstract Taxonomic relationship: Type member of the Bromovirus genus, family Bromoviridae. A member of the alphavirus-like supergroup of positive-sense single-stranded RNA viruses. Physical properties: Virions are nonenveloped icosahedrals made up of 180 coat protein subunits (Fig. 1). The particles are 26 nm in diameter and contain 22% nucleic acid and 78% protein. The BMV genome is composed of three positive-sense, capped RNAs: RNA1 (3.2 kb), RNA2 (2.9 kb), RNA3 (2.1 kb) (Fig. 2). Viral proteins: RNA1 encodes protein 1a, containing capping and putative RNA helicase activities. RNA2 encodes protein 2a, a putative RNA-dependent RNA polymerase. RNA3 codes for two proteins: 3a, which is required for cell-to-cell movement, and the capsid protein. The capsid is translated from a subgenomic RNA, RNA4 (1.2 kb). Hosts: Monocots in the Poacea family, including Bromus inermis, Zea mays and Hordeum vulgare, in which BMV causes brown streaks. BMV can also infect the dicots Nicotiana benthamiana and several Chenopodium species. In N. benthamiana, the infection is asymptomatic while infection of Chenopodium can cause either necrotic or chlorotic lesions. Useful website:http://www4.ncbi. nlm.nih. gov/ICTVdb/ICTVdB/10030001.htm.
1‐n‐Hexadecyl‐3‐methylimidazolium methanesulfonate and chloride salts with effective activities against Candida tropicalis biofilms

Although the use of catheters in critically ill patients is mostly inevitable, this invasive procedure comes together with several health risks. Within this context, the contamination with Candida tropicalis is a primary concern as this highly prevalent pathogenic yeast can develop an extensive polymeric matrix that hinders the drugs' penetration and its effective treatment. This study addresses the potential for the 1‐n‐hexadecyl‐3‐methylimidazolium methanesulfonate (C16MImMeS) and chloride (C16MImCl) salts for eliminating the viable cells of biofilms of Candida tropicalis, compared to the performance of chlorhexidine (CHX) and fluconazole (FLZ). The minimum concentration required of C16MImMeS, C16MImCl, CHX and FLZ for elimination of the biofilm′s viable cells (MBEC) was evaluated through microtitre plate biofilm exposure with different concentrations of these substances. These concentrations were determined at 80% of effective activity against the biofilm′s viable cells by using the MTT reduction assay. C16MImMeS and C16MImCl were able to eliminate the viable cells at much lower concentrations (15·6 and 0·45 μg ml−1 respectively) than CHX (1250 μg ml−1) and FLZ (resistance of the viable cells). This demonstrates the high potential of these substances for nosocomial infections control.
Impact of stress on menstrual cycle: A comparison between medical and non medical students

Introduction: In the wake of fast paced life and cut throat competitions, students are under high academic pressure. Neuroendocrine system plays a vital role not only in supporting normal physiological function but also during stress. It influences the endocrine and reproductive system to help in adaptation and maintains homeostasis in response to stressors. Material and Methods: Study was done on 100 female college students (50 medical and 50 non-medicals). Based on the questionnaires each participant was evaluated for level of stress and variations in menstrual patterns like length, duration, dysmenorrhoea, premenstrual tension etc. Result: Significant association was observed between the level of stress and presence of premenstrual symptoms (P = 0.002). Higher stress was associated with passage of clots (P = 0.01), painful periods (P = 0.012) and the presence of premenstrual symptoms (P = 0.002). Higher number of medicos suffered from premenstrual symptoms compared to non-medical students (60%, 40%, P = 0.046). Conclusion: A strong association was observed between stress and premenstrual symptoms. There is no difference in medical and non-medical students either in the stress level perceived or in any of the menstrual complaints except for premenstrual tension (P = 0.046) which may be as 62% of medical students perceived above average or higher level of stress compared to 50% non-medicos.
Efficacy of disinfectants against porcine rotavirus in the presence and absence of organic matter

Rotavirus is an enteric pathogen that causes morbidity and mortality in young mammals, including pigs. Outbreaks of rotavirus on commercial farms have a significant economic impact in terms of losses in production. Effective cleaning and disinfection along with good farm management can reduce rotavirus contamination in the environment, and decrease the chance of outbreaks of disease. This study investigated the efficacy of six commercial disinfectants against MS2 bacteriophage and Group A porcine rotavirus, in the presence of high and low levels of organic matter to simulate the farm environment. A phenolic‐based disinfectant (Bi‐OO‐cyst) was effective at all levels of organic matter concentrations. Iodophore‐based disinfectants did not have a significant virucidal effect against rotavirus under any conditions. For peroxygen compound‐based disinfectants and glutaraldehyde‐based disinfectants, organic matter load made a significant difference in reducing efficacy. This highlights the importance of thorough cleaning with detergent before disinfection to reduce viral contamination on the farm and decrease rotavirus disease incidence in pigs.
The mitral L wave: a marker of advanced diastolic dysfunction in patients with atrial fibrillation.

BACKGROUND The prominent mid-diastolic filling wave (mitral L wave) indicates advanced diastolic dysfunction in patients in sinus rhythm. The aim of the present study was to determine the clinical implications of the mitral L wave in patients with atrial fibrillation (AF). METHODS AND RESULTS Ninety-nine consecutive non-valvular chronic persistent AF patients were enrolled. The mitral L wave was defined as a distinct mid-diastolic flow velocity following the E wave with a peak velocity>20 cm/s. The prevalence of the L wave in AF patients (34/99, 34%) was significantly higher than that observed in patients in sinus rhythm during the same study period (23/946, 2.4%, p<0.001). Patients with AF and L wave were older, more frequently female and had a slower heart rate, shorter isovolumic relaxation times, larger E wave velocities and lower early diastolic mitral annulus velocity (E') resulting in the higher E/E' compared to those without L waves. The left atrial volume index was significantly larger in patients with an L wave. The Valsalva maneuver decreased, and leg elevation increased, the amplitude of the L wave in the subset of patients who received these procedures. CONCLUSIONS The appearance of the mitral L wave in AF is relatively common, and its presence indicates advanced diastolic dysfunction, including elevated filling pressures and distended noncompliant LA.
Pseudonocardia tropica sp. nov., an endophytic actinomycete isolated from the stem of Maytenus austroyunnanensis.

A novel strain, designated YIM 61452(T), was isolated from the stem of Maytenus austroyunnanensis collected from the tropical rainforest of Xishuangbanna, Yunnan Province, south-west China. The strain was characterized taxonomically by using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM 61452(T) belonged to the genus Pseudonocardia and was most closely related to Pseudonocardia alni IMSNU 20049(T) (99.5 %), Pseudonocardia antarctica DVS 5a1(T) (99.5 %) and Pseudonocardia carboxydivorans Y8(T) (99.4 %). The chemotaxonomic properties of strain YIM 61452(T), for example MK-8(H(4)) as the predominant quinone system and iso-C(16 : 0) and iso-C(16 : 1) H as the major fatty acids, were also consistent with its classification within the genus Pseudonocardia. Strain YIM 61452(T) could be differentiated from closely related species of the genus Pseudonocardia by phenotypic and genotypic analysis. DNA-DNA hybridization experiments between strain YIM 61452(T) and closely related reference strains further confirmed that strain YIM 61452(T) represented a novel taxon of the genus Pseudonocardia. Therefore, strain YIM 61452(T) represents a novel species, for which the name Pseudonocardia tropica sp. nov. is proposed. The type strain is YIM 61452(T) (=DSM 45199(T)=CCTCC AA 208018(T)).
Beneficial effects of live and dead Salmonella‐based vector strain on the course of colitis in mice

Dysbiosis of intestinal microbiota and hyperactive immune responses seem to be crucial for the uncontrolled inflammation in inflammatory bowel diseases (IBD). Modulation of the microbiome and immune stimulation of the intestinal epithelium were suggested as therapeutic approaches. In this study, live attenuated and dead bacterial cells of Salmonella Typhimurium SL7207 – a widely used bacterial vector for gene therapy were administered in DSS‐induced colitis in mice. C57BL/6 mice were divided into four groups. The first group received pure water (CTRL). The other three groups received 2% dextran sulphate sodium (DSS) to induce colitis. Two DSS groups were treated with live attenuated (DSS live) or inactivated (DSS dead) Salmonella by gastric gavage. Intake of 2% DSS caused weight loss in all DSS groups compared to control mice with some improvement in DSS live group on the last day of the experiment. Significantly longer colon and improved stool consistency were reported in DSS live group, but not DSS dead group, when compared with DSS. Significant enlargement of spleens was observed only in DSS and DSS dead groups compared to control. Significant differences in stool consistency, colon length and spleen enlargement were observed between DSS live and DSS dead groups with beneficial effects of live bacteria. Interestingly, significant decrease in myeloperoxidase activity was detected in both, DSS live and DSS dead groups compared to the DSS group. On the basis of these results, progression of colitis seems to be beneficially influenced not only by live attenuated but to some extent also by inactivated Salmonella Typhimurium SL7207. Our results provide evidence that Salmonella‐based gene therapy vectors are able to positively alter gut homeostasis during DSS‐induced colitis.
Microbial dynamics in anaerobic digestion reactors for treating organic urban residues during the start‐up process

Anaerobic digestion of organic residues offers economic benefits via biogas production, still methane (CH4) yield relies on the development of a robust microbial consortia for adequate substrate degradation, among other factors. In this study, we monitor biogas production and changes in the microbial community composition in two semi‐continuous stirred tank reactors during the setting process under mesophilic conditions (35°C) using a 16S rDNA high‐throughput sequencing method. Reactors were initially inoculated with anaerobic granular sludge from a brewery wastewater treatment plant, and gradually fed organic urban residues (4·0 kg VS m−3 day−1) . The inocula and biomass samples showed changes related to adaptations of the community to urban organic wastes including a higher relative proportion of Clostridiales, with Ruminococcus spp. and Syntrophomonas spp. as recurrent species. Candidatus Cloacamonas spp. (Spirochaetes) also increased from ~2·2% in the inoculum to >10% in the reactor biomass. The new community consolidated the cellulose degradation and the propionate and amino acids fermentation processes. Acetoclastic methanogens were more abundant in the reactor, where Methanosaeta spp. was found as a key player. This study demonstrates a successful use of brewery treatment plant granular sludge to obtain a robust consortium for methane production from urban organic solid waste in Mexico.
Open versus robot-assisted partial nephrectomy: effect on clinical outcome.

BACKGROUND AND PURPOSE Robot-assisted partial nephrectomy (RPN) has emerged as a viable alternative to open partial nephrectomy (OPN) for small renal masses (SRMs). Comparative outcomes of RPN and OPN at a single institution were analyzed. PATIENTS AND METHODS A retrospective review was performed to compare 69 RPNs with 234 OPNs between May 2003 and December 2010 at a single institution. Clinicopathologic variables, operative parameters, and renal functional outcomes were analyzed. RESULTS There were no significant differences between the two cohorts (RPN vs OPN) with respect to patient age (P=0.609), sex (P=0.703), preoperative estimated glomerular filtration rate (eGFR, P=0.146), estimated blood loss (P=0.600), and tumor size (P=0.256). The mean operative time was longer in the RPN group (192 vs 142 min, P<0.001). The mean warm ischemia time was longer in the RPN cohort (22.99 vs 18.87 min, P<0.001), but there were no significant differences in the postoperative eGFR (P=0.162) and change in the eGFR (P=0.520). The length of hospitalization (6.2 vs 8.9 d, P<0.001) and use of postoperative analgesics (ketoprofen, 0.26 vs 0.88 ampules, P<0.001) were more favorable in the RPN cohort. The number of patients with positive surgical margins was 0 for the RPN and 6 for the OPN groups. The intraoperative complication rates were 4.35% and 4.27% in the RPN and OPN groups, respectively (P=0.999). The overall postoperative complication rates were 8.7% and 15.4% in the RPN and OPN groups, respectively (P=0.158). CONCLUSIONS RPN is a viable option as a nephron-sparing surgical procedure for SRMs considering the perioperative parameters and postoperative renal function changes, in addition to the traditional benefits of the laparoscopic procedure.
Perioperative patient radiation exposure in the endoscopic removal of upper urinary tract calculi.

BACKGROUND AND PURPOSE The efficacy of computed tomography (CT) in detailing upper urinary tract calculi is well established. There is no established acceptable annual recommended limit for medical exposure, yet the global accepted upper limit for occupational radiation exposure is <50 millisieverts (mSv) in any one year. We sought to appreciate the CT and fluoroscopic radiation exposure to our patients undergoing endoscopic removal of upper tract calculi during the periprocedure period. PATIENTS AND METHODS All patients undergoing upper urinary endoscopic stone removal between 2005 and 2009 were identified. To calculate the cumulative radiation exposure, we included all ionizing radiation imaging performed during a periprocedure period, which we defined as ≤90 days pre- and post-therapeutic procedure. RESULTS A total of 233 upper urinary tract therapeutic patient stone procedures were identified; 127 patients underwent ureteroscopy (URS) and 106 patients underwent percutaneous nephrolithotomy (PCNL). A mean 1.58 CTs were performed per patient. Ninety (38.6%) patients underwent ≥2 CTs in the periprocedure period, with an average number in this group of 2.49 CT/patient, resulting in approximately 49.8 mSv of CT radiation exposure. Patients who were undergoing URS were significantly more likely to have multiple CTs (P=0.003) than those undergoing PCNL. Median fluoroscopic procedure exposures were 43.3 mGy for patients who were undergoing PCNL and 27.6 mGy for those patients undergoing URS. CONCLUSIONS CT radiation exposure in the periprocedure period for patients who were undergoing endoscopic upper tract stone removal is considerable. Added to this is the procedure-related fluoroscopic radiation exposure. Urologic surgeons should be aware of the cumulative amount of ionizing radiation received by their patients from multiple sources.
Ecology and identification of environmental fungi and metabolic processes involved in the biodeterioration of Brazilian soapstone historical monuments

This study aimed to evaluate the action of organic acids produced by the fungal population associated with the biodeterioration process of the Twelve Prophets of Aleijadinho, a set of soapstone sculptures in Congonhas, state of Minas Gerais, Brazil. For this, samples of fungi were obtained from the surface of each of the 12 outdoor stone sculptures that comprise the set of Prophets. The identification of the colonizing filamentous fungi was performed by classical microbiology and molecular methods. Some species of filamentous fungi‐dependent cultivation were detected, and the presence of species Aspergillus versicolor, Curvularia lunata, Epicoccum nigrum, Penicillium citrinum and Pseudocercospora norchiensis indicated a connection with the excretion of organic acids. The acids produced by each of these fungal species were analysed quantitatively by chromatographic methods, revealing potential biodeterioration by the action of acidic metabolites excreted in the stone.