Indian agriculture, air pollution, and public health in the age of COVID.

Emerging evidence supports the intuitive link between chronic health conditions associated with air pollution and the vulnerability of individuals and communities to COVID-19. Poor air quality already imposes a highly significant public health burden in Northwest India, with pollution levels spiking to hazardous levels in November and early December when rice crop residues are burned. The urgency of curtailing the COVID-19 pandemic and mitigating a potential resurgence later in the year provides even more justification for accelerating efforts to dramatically reduce open agricultural burning in India.

Validation of MALDI-TOF MS Biotyper database optimized for anaerobic bacteria: The ENRIA project.

Within the ENRIA project, several 'expertise laboratories' collaborated in order to optimize the identification of clinical anaerobic isolates by using a widely available platform, the Biotyper Matrix Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS). Main Spectral Profiles (MSPs) of well characterized anaerobic strains were added to one of the latest updates of the Biotyper database db6903; (V6 database) for common use. MSPs of anaerobic strains nominated for addition to the Biotyper database are included in this validation. In this study, we validated the optimized database (db5989 [V5 database] + ENRIA MSPs) using 6309 anaerobic isolates. Using the V5 database 71.1% of the isolates could be identified with high confidence, 16.9% with low confidence and 12.0% could not be identified. Including the MSPs added to the V6 database and all MSPs created within the ENRIA project, the amount of strains identified with high confidence increased to 74.8% and 79.2%, respectively. Strains that could not be identified using MALDI-TOF MS decreased to 10.4% and 7.3%, respectively. The observed increase in high confidence identifications differed per genus. For Bilophila wadsworthia, Prevotella spp., gram-positive anaerobic cocci and other less commonly encountered species more strains were identified with higher confidence. A subset of the non-identified strains (42.1%) were identified using 16S rDNA gene sequencing. The obtained identities demonstrated that strains could not be identified either due to the generation of spectra of insufficient quality or due to the fact that no MSP of the encountered species was present in the database. Undoubtedly, the ENRIA project has successfully increased the number of anaerobic isolates that can be identified with high confidence. We therefore recommend further expansion of the database to include less frequently isolated species as this would also allow us to gain valuable insight into the clinical relevance of these less common anaerobic bacteria.

A multi-center ring trial for the identification of anaerobic bacteria using MALDI-TOF MS.

Inter-laboratory reproducibility of Matrix Assisted Laser Desorption Time-of-Flight Mass Spectrometry (MALDI-TOF MS) of anaerobic bacteria has not been shown before. Therefore, ten anonymized anaerobic strains were sent to seven participating laboratories, an initiative of the European Network for the Rapid Identification of Anaerobes (ENRIA). On arrival the strains were cultured and identified using MALDI-TOF MS. The spectra derived were compared with two different Biotyper MALDI-TOF MS databases, the db5627 and the db6903. The results obtained using the db5627 shows a reasonable variation between the different laboratories. However, when a more optimized database is used, the variation is less pronounced. In this study we show that an optimized database not only results in a higher number of strains which can be identified using MALDI-TOF MS, but also corrects for differences in performance between laboratories.

Investigation of Hungarian mushrooms for antibacterial activity and synergistic effects with standard antibiotics against resistant bacterial strains.

UNLABELLED: This study aimed to screen the antibacterial activity of 160 extracts of 40 mushroom species, collected in Hungary, against 11 standard bacterial strains and 9 clinical isolates. The further objective of this work was to evaluate the capacity of active fungal extracts to potentiate the action of antibiotics against resistant pathogens. Disc-diffusion method was applied for screening of antibacterial activity of extracts. Microdilution method was used to determine minimum inhibitory concentrations. The active extracts were applied to different resistant micro-organisms (multiresistant Acinetobacter baumannii and Pseudomonas aeruginosa, vancomycin-resistant Enterococcus faecium and MRSA), combined with commercial drugs. The synergism between extracts and antibiotics was assessed by double-disc synergy assay and determination of fractional inhibitory concentration (FIC) with checkerboard technique. From 40 mushrooms included in this experiment, 16 species exhibited antibacterial effects with moderate to high potential. In general the chloroform extracts proved to be most active, while the aqueous and aqueous-methanolic extracts demonstrated low or no activity. Fistulina hepatica, Tapinella atrotomentosa (syn. Paxillus atrotomentosus) and Rhodocybe popinalis were the most active species; moreover, they can potentiate the action of cefuroxime against MRSA. SIGNIFICANCE AND IMPACT OF THE STUDY: In this study, 160 organic (n-hexane, chloroform and 50% methanol) and aqueous extracts of 40 mushroom species were submitted to antibacterial screening assay. The antibacterial capacity of 18 species has been examined for the first time. Nineteen extracts of 16 species showed antibacterial effects with moderate to high potential. The extracts of Fistulina hepatica, Tapinella atrotomentosa and Rhodocybe popinalis exhibited not only broad antibacterial spectrum, but also synergistic activity with cefuroxime against MRSA. Our screening study proved that mushroom species are promising sources of potential antimicrobial molecules. The results serve as good starting point for selection of fungal species for detailed pharmacological and chemical investigation.

No improvement of survival with reduced- versus high-intensity conditioning for allogeneic stem cell transplants in Ewing tumor patients.

BACKGROUND: Outcomes of Ewing tumor (ET) patients treated with allogeneic stem cell transplantation (allo-SCT) were compared regarding the use of reduced-intensity conditioning (RIC) and high-intensity conditioning (HIC) regimens as well as human leukocyte antigen (HLA)-matched and HLA-mismatched grafts. PATIENTS AND METHODS: We retrospectively analyzed data of 87 ET patients from the European Group for Blood and Marrow Transplantation, Pediatric Registry for Stem Cell Transplantations, Asia Pacific Blood and Marrow Transplantation and MetaEICESS registries treated with allo-SCT. Fifty patients received RIC (group A) and 37 patients received HIC (group B). Twenty-four patients received HLA-mismatched grafts and 63 received HLA-matched grafts. RESULTS: Median overall survival was 7.9 months [±1.24, 95% confidence interval (CI) 5.44-10.31] for group A and 4.4 months (±1.06, 95% CI 2.29-6.43) for group B patients (P = 1.3). Death of complications (DOC) occurred in 4 of 50 (0.08) and death of disease (DOD) in 33 of 50 (0.66) group A and in 16 of 37 (0.43) and 17 of 37 (0.46) group B patients, respectively. DOC incidence was decreased (P < 0.01) and DOD/relapse increased (P < 0.01) in group A compared with group B. HLA mismatch was not generally associated with graft-versus-Ewing tumor effect (GvETE). CONCLUSIONS: There was no improvement of survival with RIC compared with HIC due to increased DOD/relapse incidence after RIC despite less DOC incidence. This implicates general absence of a clinically relevant GvETE with current protocols.

Demonstration of a neutral atom controlled-NOT quantum gate.

We present the first demonstration of a CNOT gate between two individually addressed neutral atoms. Our implementation of the CNOT uses Rydberg blockade interactions between neutral atoms held in optical traps separated by >8 microm. Using two different gate protocols we measure CNOT fidelities of F=0.73 and 0.72 based on truth table probabilities. The gate was used to generate Bell states with fidelity F=0.48+/-0.06. After correcting for atom loss we obtain an a posteriori entanglement fidelity of F=0.58.

Biologicl activity and synthesis of an encephalitogenic determinant.

A 45-residue fragment of the basic protein of myelin is encephalitogenic in the rabbit and monkey but relatively inactive in the guinea pig. Synthetic peptides containing the sequence of a tryptic peptide of the fragment Thr-Thr-His-Tyr-Gly-Ser-Leu-Pro-Gln-Lys are moderately encephalitogenic.

Impact of EUCAST ceftaroline breakpoint change on the susceptibility of methicillin-resistant Staphylococcus aureus isolates collected from patients with complicated skin and soft-tissue infections.

OBJECTIVES: In 2018, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) introduced an intermediate breakpoint for ceftaroline against Staphylococcus aureus. The objective of this study was to compare data on resistance to ceftaroline among methicillin-resistant S. aureus (MRSA) isolates using versions 7.1 (March 2017) and 8.0 (January 2018) of the EUCAST breakpoints. METHODS: Participating centers were located in Africa, Asia, Europe, Oceania and South America. Isolates were collected from patients with complicated skin and soft-tissue infections and were cultured from integumentary sources. Methicillin resistance among S. aureus was confirmed locally using the oxacillin method. The CLSI broth microdilution method was used to measure ceftaroline MICs at the central laboratory. Versions 7.1 and 8.0 of the EUCAST breakpoints were used to interpret MIC data. RESULTS: Between 2015 and 2016, 9559 isolates of S. aureus were collected, of which 5566 (58.2%) isolates were MRSA. Overall, the lowest rate of MRSA was in Asia (56.5%; 705/1247) and the highest rate was in Oceania (62.7%; 299/477). Using version 7.1 of the EUCAST breakpoints, 4.5% (250/5566) of all MRSA isolates were resistant to ceftaroline and when version 8.0 of the breakpoints was applied, 4.2% (235/5566) of MRSA were in the intermediate category and 0.3% (15/5566) of all isolates were considered resistant. CONCLUSIONS: By applying version 8.0 of the EUCAST breakpoints, the majority of MRSA isolates that were resistant are now in the intermediate category for ceftaroline. Ceftaroline resistance among MRSA now appears rare.

Characterization of Pasteurella multocida strains isolated from human infections.

Isolates of Pasteurella multocida recovered from infected humans (n = 15) were characterized by traditional and molecular microbiological methods and were compared with cat-derived strains (n = 5). The most prevalent subspecies among strains from human infections was P. multocida subsp. septica (80%), and nearly all isolates showed a similar combination of virulence-associated genes. MLST analysis classified the 20 P. multocida strains into 16 different sequence types, and we assigned 11 new sequence types (ST), however, only one of those (ST 334) was shared by two human and one cat isolates. P. multocida subsp. septica strains formed a distinct phylogenetic group within the species. The strains showed resistance to erythromycin, clindamycin and sulfamethoxazole, and with two exceptions, resistance to tilmicosin was also detected. Each strain was susceptible to ampicillin, streptomycin, gentamycin, tetracycline, doxycycline, cefazolin, cefpodoxime, chloramphenicol, florfenicol and enrofloxacin. Common characteristics (virulence profile and antibiotic sensitivity pattern) shared by strains isolated from humans and cats support the view that domestic cats may serve as a potential reservoir for P. multocida.

Filopodia formation induced by active mDia2/Drf3.

Filopodia are rod-shaped cell surface protrusions composed of a parallel bundle of actin filaments. Since filopodia frequently emanate from lamellipodia, it has been proposed that they form exclusively by the convergence and elongation of actin filaments generated in lamellipodia networks. However, filopodia form without Arp2/3-complex, which is essential for lamellipodia formation, indicating that actin filaments in filopodia may be generated by other nucleators. Here we analyzed the effects of ectopic expression of GFP-tagged full length or a constitutively active variant of the human formin mDia2/Drf3. By contrast to the full-length molecule, which did not affect cell behaviour and was entirely cytosolic, active Drf3 lacking the C-terminal regulatory region (Drf3DeltaDAD) induced the formation of filopodia and accumulated at their tips. Low expression of Drf3DeltaDAD induced rod-shaped or tapered filopodia, whereas over-expression resulted in multiple, club-shaped filopodia. The clubs were filled with densely bundled actin filaments, whose number but not packing density decreased further away from the tip. Interestingly, clubs frequently increased in width after protrusion beyond the cell periphery, which correlated with increased amounts of Drf3DeltaDAD at their tips. These data suggest Drf3-induced filopodia form and extend by de novo nucleation of actin filaments instead of convergent elongation. Finally, Drf3DeltaDAD also induced the formation of unusual, lamellipodia-like structures, which contained both lamellipodial markers and the prominent filopodial protein fascin. Microarray analyses revealed highly variable Drf3 expression levels in different commonly used cell lines, reflecting the need for more detailed analyses of the functions of distinct formins in actin cytoskeleton turnover and different cell types.

Lyotropic liquid crystal preconcentrates for the treatment of periodontal disease.

The aim of our study was to develop water-free lyotropic liquid crystalline preconcentrates, which consist of oils and surfactants with good physiological tolerance and spontaneously form lyotropic liquid crystalline phase in aqueous environment. In this way these preconcentrates having low viscosity can be injected into the periodontal pocket, where they are transformed into highly viscous liquid crystalline phase, so that the preparation is prevented from flowing out of the pocket due to its great viscosity, while drug release is controlled by the liquid crystalline texture. In order to follow the structure alteration upon water absorption polarization microscopical and rheological examinations were performed. The water absorption mechanism of the samples was examined by the Enslin-method. Metronidazole-benzoate was used as active agent the release of which was characterized via in vitro investigations performed by means of modified Kirby-Bauer disk diffusion method. On the grounds of the results it can be stated that the 4:1 mixture of the investigated surfactants (Cremophor EL, Cremophor RH40) and oil (Miglyol 810) formed lyotopic liquid crystalline phases upon water addition. Polarization microscopic examinations showed that samples with 10-40% water content possessed anisotropic properties. On the basis of water absorption, rheological and drug release studies it can be concluded that the amount of absorbed water and stiffness of lyotropic structure influenced by the chemical entity of the surfactant exerted major effect on the drug release.

An overview of the data obtained during the validation of an optimized MALDI-TOF MS Biotyper database for the identification of anaerobic bacteria.

This data in brief article presents the data obtained during the validation of the optimized Biotyper Matrix Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) database. The validation was performed by the different expertise laboratories, collaborating within the European Network for the Rapid Identification of Anaerobes (ENRIA) project, using 6309 human clinical anaerobic bacterial strains. Different databases were compared with each other; the db 5989 database (V5 database); the V5 database complimented with Main Spectral Profiles (MSPs) of ENRIA strains added to the next update of the database; and the V5 database complimented with the MSPs of all anaerobic clinical isolates collected within the ENRIA project. For a comprehensive discussion of the full dataset, please see the research article that accompanies this data article (Veloo et al., 2018) [1].

The optimization and validation of the Biotyper MALDI-TOF MS database for the identification of Gram-positive anaerobic cocci.

Gram-positive anaerobic cocci (GPAC) account for 24%-31% of the anaerobic bacteria isolated from human clinical specimens. At present, GPAC are under-represented in the Biotyper MALDI-TOF MS database. Profiles of new species have yet to be added. We present the optimization of the matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS) database for the identification of GPAC. Main spectral profiles (MSPs) were created for 108 clinical GPAC isolates. Identity was confirmed using 16S rRNA gene sequencing. Species identification was considered to be reliable if the sequence similarity with its closest relative was ≥98.7%. The optimized database was validated using 140 clinical isolates. The 16S rRNA sequencing identity was compared with the MALDI-TOF MS result. MSPs were added from 17 species that were not yet represented in the MALDI-TOF MS database or were under-represented (fewer than five MSPs). This resulted in an increase from 53.6% (75/140) to 82.1% (115/140) of GPAC isolates that could be identified at the species level using MALDI-TOF MS. An improved log score was obtained for 51.4% (72/140) of the strains. For strains with a sequence similarity <98.7% with their closest relative (n = 5) or with an inconclusive sequence identity (n = 4), no identification was obtained by MALDI-TOF MS or in the latter case an identity with one of its relatives. For some species the MSP of the type strain was not part of the confined cluster of the corresponding clinical isolates. Also, not all species formed a homogeneous cluster. It emphasizes the necessity of adding sufficient MSPs of human clinical isolates.

Biofilm formation on intrauterine devices in relation to duration of use.

Intrauterine devices (IUDs) are highly effective, long-term methods of contraception; however, IUD use is limited due to concerns about an increased risk of pelvic inflammatory disease (PID) and subsequent complications. A retrospective review of clinical and microbiological data of 127 participants was carried out over a 3 year period. IUDs were removed and sent for microbiological examination. A 10 year old IUD, removed because of the symptoms of PID, was investigated via both microbial culture and scanning electron microscopy. The primary objective of this study was to examine the bacteria present on removed IUDs after different times in situ by using aerobic and anaerobic culture methods. A close association of the distribution of aerobic and anaerobic bacteria on the IUDs with different times in situ was found.

Copper absorption by remnant small bowel after extensive intestinal resection in the rat.

Rats were subjected to 50% proximal or 50% distal small bowel resection or sham operation. Four weeks later intestinal absorption of copper was measured in vivo using a recirculation technique. In each rat 10 cm in situ segments of duodenum, midgut, and ileum were perfused through the lumen for 2 h with 15 ml of an isotonic solution containing 2 micrograms/ml copper together with 14C-polyethylene glycol as volume marker. Absorption was expressed per g dry mucosa and per cm segment length. After proximal enterectomy absorption of copper per g mucosa decreased in the duodenum and midgut but remained unchanged in the ileum compared to sham-operated controls. However, there were adaptive increases in mucosal mass in all segments. Copper absorption per cm segment length in duodenum and midgut remained unchanged from controls and ileal absorption per cm increased in proportion to mucosal growth. After distal enterectomy absorption of copper per g mucosa remained unchanged in the duodenum but decreased in the midgut and ileum compared to sham-operated controls. Adaptive mucosal growth now occurred only in the midgut and ileum. In the ileum mucosal mass more than doubled. Copper absorption per cm segment length in the duodenum and midgut did not change from controls. However, in the ileum absorption per cm increased above that of controls because of the marked mucosal growth. Therefore, in response to either proximal or distal small bowel resection, the ileum was the site for adaptive copper absorption but adaptive mechanisms differed.(ABSTRACT TRUNCATED AT 250 WORDS)

Concurrent cerebral venous sinus thrombosis and myeloradiculopathy in Sjögren's syndrome.

A 41-year-old woman complained of severe headaches and developed quadriparesis and neurogenic bladder. Evaluation disclosed the presence of Sjögren's syndrome complicated by myeloradiculopathy with MRI evidence of cervical cord involvement. Concurrent cerebral venous sinus thrombosis was also noted. Treatment with steroids and warfarin led to clinical improvement and resolution of MRI findings.

Post-irradiation neuromyotonia affecting trigeminal nerve distribution: an unusual presentation.

We describe two patients who developed neuromyotonia of the floor of the mouth after irradiation of a motor branch (V3) of the trigeminal nerve. The neuromyotonia manifested as sustained muscle contraction due to peripheral nerve dysfunction. The neuromyotonia in both patients was controlled with carbamazepine. Radiation-exposed nerves can become symptomatic months or years after completion of radiation therapy.

Prevalence of the carbapenemase gene (cfiA) among clinical and normal flora isolates of Bacteroides species in Hungary.

The carbapenemase gene (cfiA) was detected in 4 (5.7%) of 70 clinical isolates of Bacteroides fragilis from different parts of Hungary. Among 24 other Bacteroides species isolated from infectious processes or from normal faecal flora, none was cfiA-positive. The MIC of imipenem and meropenem for all cfiA-positive B. fragilis isolates was < or =0.25 mg/L, but 17% of the B. fragilis and 46% of the non-fragilis Bacteroides isolates exhibited reduced susceptibility to imipenem (MICs 0.5-2 mg/L). Only one of these isolates produced increased levels of beta-lactamase. No difference was observed in the outer-membrane proteins of B. fragilis isolates that harboured the cfiA gene and those with reduced susceptibility to imipenem.

Prevalence of gastrointestinal disease caused by Clostridium difficile in a university hospital in Hungary.

A one-year survey was undertaken to investigate the frequency of diarrhoea caused by Clostridium difficile among patients in a 1200-bed university hospital in Hungary. The VIDAS (bioMérieux) toxin A detection kit was used for screening specimens for the presence of C. difficile toxin. For all other diarrhoeal specimens selected according to special criteria, cytotoxin testing was used to determine the presence of 'free toxin' in the faeces. During the study period, a total of 945 diarrhoeal faecal samples were tested for the presence of C. difficile toxin. Of 375 requested samples, 58 (18.3%) were toxin-A positive. Of the 570 remaining faecal samples selected by the laboratory, 120 (21%) proved to be toxin positive. The results showed that patients from the surgical (33.3%), internal (24%) and haematological (12.8%) wards had the greatest frequency of diarrhoea attributable to C. difficile.

Why make monofilament sutures out of polyvinylidene fluoride?

In recent years some clinical reports have associated suture failures with polypropylene monofilaments. Therefore there is interest in developing an alternative suture material that is less thrombogenic than polyester and similar in handling characteristics but less prone to mechanical failure than polypropylene. To this end, Peters Laboratoire Pharmaceutique has developed a new monofilament suture material from polyvinylidene fluoride (PVDF), which has been subjected to a special treatment to modify its crystalline form and level of crystallinity. The purpose of this study was to evaluate its mechanical, chemical, and biologic properties and to compare its performance, in a peripheral vascular application, to that of a polypropylene control. A series of in vitro tests were performed to study the morphology, tensile properties, creep, surface chemistry, thermal characteristics, and resistance to iatrogenic trauma. In addition, an in vivo trial was undertaken in which vascular prostheses anastomosed with either PVDF or polypropylene sutures were implanted as a thoracoabdominal bypass for 6 months in the dog. Histologic and degradation analyses were performed on the explants. The results from the mechanical tests on 4-0, 5-0, and 6-0 PVDF and polypropylene sutures demonstrated that although both materials have similar breaking strengths, the PVDF has a higher extension at break, has less delayed extension when under tensile creep testing, and suffers less trauma than the polypropylene when compressed by a standard needle holder. While chemical analyses found evidence of surface oxidation on both types of sutures, thermal analysis confirmed that the level of crystallinity of the PVDF polymer is higher than that of the polypropylene control. During the pilot study in animals, PVDF sutures were found to have good handling and frictional characteristics that facilitated the tying of knots. Histologic analysis of the explants found no inflammatory cells in the tissue surrounding either the PVDF or polypropylene sutures, and scanning electron microscopic examination of the cleaned suture surfaces found no evidence of degradation during 6 months in vivo. Though preliminary in nature, these findings indicate that monofilament sutures made from PVDF provide an attractive alternative to those made from polypropylene for use in cardiovascular surgery. In addition to providing acceptable in vivo behavior and being easy to manipulate and more resistant to iatrogenic injury, PVDF materials can be sterilized by beta or gamma radiation and so can reduce dependence upon ethylene oxide and chlorofluorohydrocarbons.