Efficiency of Different Disinfectants on Bacillus cereus Sensu Stricto Biofilms on Stainless-Steel Surfaces in Contact With Milk

The species of the Bacillus cereus group have the ability to adhere to and form biofilms on solid surfaces, including stainless steel, a material widely used in food industries. Biofilms allow for recontamination during food processing, and the “clean-in-place” (CIP) system is largely used by industries to control them. This study thus proposes to evaluate the efficacy of peracetic acid and sodium hypochlorite against biofilms induced on stainless-steel surfaces. The SAMN07414939 isolate (BioProject PRJNA390851), a recognized biofilm producer, was selected for biofilm induction on AISI 304 stainless steel. Biofilm induction was performed and classified into three categories: TCP (Tindalized, Contaminated, and Pasteurized milk), TCS (Tindalized milk Contaminated with Spores), and TCV (Tindalized milk Contaminated with Vegetative cells). Subsequently, the coupons were sanitized simulating a CIP procedure, on a pilot scale, using alkaline and acid solutions followed by disinfectants (peracetic acid and sodium hypochlorite). Microorganism adhesion on the surfaces reached 6.3 × 105 to 3.1 × 107 CFU/cm-2. Results did not show significant differences (p > 0.05) for surface adhesion between the three tested categories (TCP, TCS, and TCV) or (p > 0.05) between the two disinfectants (peracetic acid and sodium hypochlorite). Microbial populations adhered to the stainless-steel coupons are equally reduced after treatment with peracetic acid and sodium hypochlorite, with no differences in the control of B. cereuss.s. biofilms on AISI 304 stainless-steel surfaces

Temporal trend of tuberculosis incidence and its spatial distribution in Macapá – Amapá

OBJETIVO: Avaliar a tendência temporal da incidência da tuberculose após a implementação do teste rápido molecular, identificar se a tuberculose apresenta variação sazonal e classificar o território de acordo com a densidade de casos e as áreas de risco em Macapá-AP. MÉTODOS: Estudo ecológico composto por casos de tuberculose registrados no SINAN entre 2001 e 2017. Foi utilizado o teste Prais-Winsten para classificar a tendência temporal da incidência e a Série Temporal Interrompida para identificar mudanças na tendência temporal antes e depois da implementação do teste rápido molecular, além de verificar a sazonalidade no município. Utilizou-se o estimador de Kernel para classificar a densidade de casos e estatística de varredura para identificar áreas de risco da tuberculose. RESULTADOS: Foram identificados 1730 casos, observando-se que a tendência temporal da incidência de tuberculose foi decrescente (-0,27% por mês, IC95% −0,13 a −0,41). Não houve mudança de nível na série temporal após a implantação do teste molecular GeneXpert® MTB/RIF, porém, o período pós teste foi classificado como crescente em termos da incidência (+2,09% por mês, IC95% 0,92 a 3,27). Quanto à variação sazonal, apresentou crescimento (+13,7%/mês, IC95% 4,71 a 23,87) nos meses de dezembro a junho, referente ao período de chuvas – chamado inverno amazônico – e decréscimo (-9,21% por mês, IC95% −1,37 a −16,63) nos demais períodos. Por meio de Kernel, foram classificadas áreas com alta densidade de casos nos distritos Central e Norte e, com a estatística de varredura, foram identificados três aglomerados de proteção, AE1 (RR = 0,07), AE2 (RR = 0,23) e AE3 (RR = 0,36), e um aglomerado de alto risco, AE4 (RR = 1,47). CONCLUSÃO: A tendência temporal da incidência de tuberculose se revelou decrescente na série temporal, todavia, um crescimento na detecção foi observado após introdução do TRM-TB, e ainda se evidenciou que há comportamento sazonal da tuberculose. A distribuição dos casos foi heterogênea, com tendência de concentração em territórios vulneráveis e de risco, evidenciando um padrão de desigualdade da doença no território.OBJECTIVE: To evaluate the temporal trend of tuberculosis incidence after the implementation of the rapid molecular test (RMT-TB), to identify whether tuberculosis presents seasonal variation and to classify the territory according to case density and risk areas in Macapá, Amapá. METHODS: Ecological study of tuberculosis cases registered in the Sistema de Informação de Agravos de Notificação (SINAN – Information System for Notifiable Diseases) between 2001 and 2017. We used the Prais-Winsten test to classify the temporal trend of incidence and the interrupted time series to identify changes in the temporal trend before and after the implementation of the rapid molecular test, and to verify seasonality in the municipality. The Kernel estimator was used to classify case density and scan statistics to identify areas of tuberculosis risk. RESULTS: A total of 1,730 cases were identified, with a decreasing temporal trend of tuberculosis incidence (−0.27% per month, 95%CI −0.13 to −0.41). The time series showed no change in level after the implementation of the GeneXpert®MTB/RIF molecular test; however, the incidence increased in the post-test period (+2.09% per month, 95%CI 0.92 to 3.27). Regarding the seasonal variation, it showed growth (+13.7%/month, 95%CI 4.71 to 23.87) from December to June, the rainy season – called amazon winter season –, and decrease (−9.21% per month, CI95% −1.37 to −16.63) in the other periods. We classified areas with high density of cases in the Central and Northern districts using Kernel and identified three protection clusters, SC1 (RR = 0.07), SC2 (RR = 0.23) and SC3 (RR = 0.36), and a high-risk cluster, SC4 (RR = 1.47), with the scan statistics. CONCLUSION: The temporal trend of tuberculosis incidence was decreasing in the time series; however, detection increased after the introduction of RMT-TB, and tuberculosis showed seasonal behavior. The case distribution was heterogeneous, with a tendency to concentrate in vulnerable and risk territories, evidencing a pattern of disease inequality in the territory

Bias correction of OMI HCHO columns based on FTIR and aircraft measurements and impact on top-down emission estimates

Spaceborne formaldehyde (HCHO) measurements constitute an excellent proxy for the sources of non-methane volatile organic compounds (NMVOCs). Past studies suggested substantial overestimations of NMVOC emissions in state-of-the-art inventories over major source regions. Here, the QA4ECV (Quality Assurance for Essential Climate Variables) retrieval of HCHO columns from OMI (Ozone Monitoring Instrument) is evaluated against (1) FTIR (Fourier-transform infrared) column observations at 26 stations worldwide and (2) aircraft in situ HCHO concentration measurements from campaigns conducted over the USA during 2012–2013. Both validation exercises show that OMI underestimates high columns and overestimates low columns. The linear regression of OMI and aircraft-based columns gives Ω$_{OMI}$=0,651 Ω$_{airc}$+2,95 x 10$^{15}$, molec. cm$^{-2}$ , with Ω$_{OMI}$ and Ω$_{airc}$ the OMI and aircraft-derived vertical columns, whereas the regression of OMI and FTIR data gives Ω$_{OMI}$= 6,59 Ω$_{FTIR}$ + 2.02 x 10$^{15}$, molec. cm$^{-2}$ . Inverse modelling of NMVOC emissions with a global model based on OMI columns corrected for biases based on those relationships leads to much-improved agreement against FTIR data and HCHO concentrations from 11 aircraft campaigns. The optimized global isoprene emissions ($\sim$ 445 Tgyr$^{-1}$) are 25 % higher than those obtained without bias correction. The optimized isoprene emissions bear both striking similarities and differences with recently published emissions based on spaceborne isoprene columns from the CrIS (Cross-track Infrared Sounder) sensor. Although the interannual variability of OMI HCHO columns is well understood over regions where biogenic emissions are dominant, and the HCHO trends over China and India clearly reflect anthropogenic emission changes, the observed HCHO decline over the southeastern USA remains imperfectly elucidated

TROPOMI–Sentinel-5 Precursor formaldehyde validation using an extensive network of ground-based Fourier-transform infrared stations

TROPOMI (the TROPOspheric Monitoring Instrument), on board the Sentinel-5 Precursor (S5P) satellite, has been monitoring the Earth\u27s atmosphere since October 2017 with an unprecedented horizontal resolution (initially 7 km$^{2}$×3.5 km$^{2}$, upgraded to 5.5 km$^{2}$×3.5 km$^{2}$ in August 2019). Monitoring air quality is one of the main objectives of TROPOMI; it obtains measurements of important pollutants such as nitrogen dioxide, carbon monoxide, and formaldehyde (HCHO). In this paper we assess the quality of the latest HCHO TROPOMI products versions 1.1.(5-7), using ground-based solar-absorption FTIR (Fourier-transform infrared) measurements of HCHO from 25 stations around the world, including high-, mid-, and low-latitude sites. Most of these stations are part of the Network for the Detection of Atmospheric Composition Change (NDACC), and they provide a wide range of observation conditions, from very clean remote sites to those with high HCHO levels from anthropogenic or biogenic emissions. The ground-based HCHO retrieval settings have been optimized and harmonized at all the stations, ensuring a consistent validation among the sites. In this validation work, we first assess the accuracy of TROPOMI HCHO tropospheric columns using the median of the relative differences between TROPOMI and FTIR ground-based data (BIAS). The pre-launch accuracy requirements of TROPOMI HCHO are 40 %–80 %. We observe that these requirements are well reached, with the BIAS found below 80 % at all the sites and below 40 % at 20 of the 25 sites. The provided TROPOMI systematic uncertainties are well in agreement with the observed biases at most of the stations except for the highest-HCHO-level site, where it is found to be underestimated. We find that while the BIAS has no latitudinal dependence, it is dependent on the HCHO concentration levels: an overestimation (+26±5 %) of TROPOMI is observed for very low HCHO levels (8.0×10$^{15}$ molec. cm$^{-2}$). This demonstrates the great value of such a harmonized network covering a wide range of concentration levels, the sites with high HCHO concentrations being crucial for the determination of the satellite bias in the regions of emissions and the clean sites allowing a small TROPOMI offset to be determined. The wide range of sampled HCHO levels within the network allows the robust determination of the significant constant and proportional TROPOMI HCHO biases (TROPOMI =+1.10±0.05 ×10$^{15}$+0.64±0.03 × FTIR; in molecules per square centimetre). Second, the precision of TROPOMI HCHO data is estimated by the median absolute deviation (MAD) of the relative differences between TROPOMI and FTIR ground-based data. The clean sites are especially useful for minimizing a possible additional collocation error. The precision requirement of 1.2×10$^{16}$ molec. cm$^{-2}$ for a single pixel is reached at most of the clean sites, where it is found that the TROPOMI precision can even be 2 times better (0.5–0.8×10$^{15}$ molec. cm$^{-2}$ for a single pixel). However, we find that the provided TROPOMI random uncertainties may be underestimated by a factor of 1.6 (for clean sites) to 2.3 (for high HCHO levels). The correlation is very good between TROPOMI and FTIR data (R=0.88 for 3 h mean coincidences; R=0.91 for monthly means coincidences). Using about 17 months of data (from May 2018 to September 2019), we show that the TROPOMI seasonal variability is in very good agreement at all of the FTIR sites. The FTIR network demonstrates the very good quality of the TROPOMI HCHO products, which is well within the pre-launch requirements for both accuracy and precision. This paper makes suggestions for the refinement of the TROPOMI random uncertainty budget and TROPOMI quality assurance values for a better filtering of the remaining outliers

NDACC harmonized formaldehyde time-series from 21 FTIR stations covering a wide range of column abundances

Among the more than 20 ground-based FTIR (Fourier transform infrared) stations currently operating around the globe, only a few have provided formaldehyde (HCHO) total column time series until now. Although several independent studies have shown that the FTIR measurements can provide formaldehyde total columns with good precision, the spatial coverage has not been optimal for providing good diagnostics for satellite or model validation. Furthermore, these past studies used different retrieval settings, and biases as large as 50 % can be observed in the HCHO total columns depending on these retrieval choices, which is also a weakness for validation studies combining data from different ground-based stations. For the present work, the HCHO retrieval settings have been optimized based on experience gained from past studies and have been applied consistently at the 21 participating stations. Most of them are either part of the Network for the Detection of Atmospheric Composition Change (NDACC) or under consideration for membership. We provide the harmonized settings and a characterization of the HCHO FTIR products. Depending on the station, the total systematic and random uncertainties of an individual HCHO total column measurement lie between 12 % and 27 % and between 1 and 11×1014 molec cm−2, respectively. The median values among all stations are 13 % and 2.9×1014 molec cm−2 for the total systematic and random uncertainties. This unprecedented harmonized formaldehyde data set from 21 ground-based FTIR stations is presented and its comparison with a global chemistry transport model shows consistency in absolute values as well as in seasonal cycles. The network covers very different concentration levels of formaldehyde, from very clean levels at the limit of detection (few 1013 molec cm−2) to highly polluted levels (7×1016 molec cm−2). Because the measurements can be made at any time during daylight, the diurnal cycle can be observed and is found to be significant at many stations. These HCHO time series, some of them starting in the 1990s, are crucial for past and present satellite validation and will be extended in the coming years for the next generation of satellite missions.This study has been supported by the ESA PRODEX project TROVA (2016–2018) funded by the Belgian Science Policy Office (Belspo)

NDACC harmonized formaldehyde time series from 21 FTIR stations covering a wide range of column abundances

Among the more than 20 ground-based FTIR (Fourier transform infrared) stations currently operating around the globe, only a few have provided formaldehyde (HCHO) total column time series until now. Although several independent studies have shown that the FTIR measurements can provide formaldehyde total columns with good precision, the spatial coverage has not been optimal for providing good diagnostics for satellite or model validation. Furthermore, these past studies used different retrieval settings, and biases as large as 50% can be observed in the HCHO total columns depending on these retrieval choices, which is also a weakness for validation studies combining data from different ground-based stations. For the present work, the HCHO retrieval settings have been optimized based on experience gained from past studies and have been applied consistently at the 21 participating stations. Most of them are either part of the Network for the Detection of Atmospheric Composition Change (NDACC) or under consideration for membership. We provide the harmonized settings and a characterization of the HCHO FTIR products. Depending on the station, the total systematic and random uncertainties of an individual HCHO total column measurement lie between 12% and 27% and between 1 and 11x1014 moleccm-2, respectively. The median values among all stations are 13% and 2.9x1014 moleccm-2 for the total systematic and random uncertainties. This unprecedented harmonized formaldehyde data set from 21 ground-based FTIR stations is presented and its comparison with a global chemistry transport model shows consistency in absolute values as well as in seasonal cycles. The network covers very different concentration levels of formaldehyde, from very clean levels at the limit of detection (few 1013moleccm-2) to highly polluted levels (7x1016moleccm-2). Because the measurements can be made at any time during daylight, the diurnal cycle can be observed and is found to be significant at many stations. These HCHO time series, some of them starting in the 1990s, are crucial for past and present satellite validation and will be extended in the coming years for the next generation of satellite missions

Comparative genomic survey of Bacillus cereus sensu stricto isolates from the dairy production chain in Brazil

Made available in DSpace on 2018-11-26T17:48:59Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-02-01Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)The genomes of 262 Bacillus cereus isolates were analyzed including 69 isolates sampled from equipment, raw milk and dairy products from Brazil. The population structure of isolates showed strains belonging to known phylogenetic groups II, III, IV, V and VI. Almost all the isolates obtained from dairy products belonged to group III. Investigation of specific alleles revealed high numbers of isolates carrying toxin-associated genes including cytK (53.62%), hblA (59.42%), hblC (44.93%), hblD ( 53.62%), nheA (84.06%), nheB (89.86%) and nheC (84.06%) with isolates belonging to groups IV and V having significant higher prevalence of hblACD and group IV of CytK genes. Strains from dairy products had significantly lower prevalence of CytK and hblACD genes compared to isolates from equipment and raw milk/bulk tanks. Genes related to sucrose metabolism were detected at higher frequency in isolates obtained from raw milk compared to strains from equipment and utensils. The population genomic analysis demonstrated the diversity of strains and variability of putative function among B. cereus group isolates in Brazilian dairy production, with large numbers of strains potentially able to cause foodborne illness. This detailed information will contribute to targeted interventions to reduce milk contamination and spoilage associated with B. cereus in Brazil.Univ Estadual Paulista, UNESP, Dept Med Vet Prevent & Reprod Anim, FCAV, Via Acesso Paulo Castellane S-N, BR-14884900 Sao Paulo, BrazilUniv Sao Paulo, Dept Med Vet, FZEA, Ave Duque de Caxias Norte 225, BR-13635900 Sao Paulo, BrazilUniv Bath, Dept Biol & Biochem, Milner Ctr Evolut, 4 South,Lab 0-39, Bath BA2 7AY, Avon, EnglandSwansea Univ, Med Sch, Swansea SA2 8PP, W Glam, WalesUniv Estadual Paulista, UNESP, Dept Med Vet Prevent & Reprod Anim, FCAV, Via Acesso Paulo Castellane S-N, BR-14884900 Sao Paulo, BrazilFAPESP: 2014/13104-1FAPESP: 2015/20874-0FAPESP: 2016/19214-

Effect of natalizumab on disease progression in secondary progressive multiple sclerosis (ASCEND). a phase 3, randomised, double-blind, placebo-controlled trial with an open-label extension

Background: Although several disease-modifying treatments are available for relapsing multiple sclerosis, treatment effects have been more modest in progressive multiple sclerosis and have been observed particularly in actively relapsing subgroups or those with lesion activity on imaging. We sought to assess whether natalizumab slows disease progression in secondary progressive multiple sclerosis, independent of relapses. Methods: ASCEND was a phase 3, randomised, double-blind, placebo-controlled trial (part 1) with an optional 2 year open-label extension (part 2). Enrolled patients aged 18–58 years were natalizumab-naive and had secondary progressive multiple sclerosis for 2 years or more, disability progression unrelated to relapses in the previous year, and Expanded Disability Status Scale (EDSS) scores of 3·0–6·5. In part 1, patients from 163 sites in 17 countries were randomly assigned (1:1) to receive 300 mg intravenous natalizumab or placebo every 4 weeks for 2 years. Patients were stratified by site and by EDSS score (3·0–5·5 vs 6·0–6·5). Patients completing part 1 could enrol in part 2, in which all patients received natalizumab every 4 weeks until the end of the study. Throughout both parts, patients and staff were masked to the treatment received in part 1. The primary outcome in part 1 was the proportion of patients with sustained disability progression, assessed by one or more of three measures: the EDSS, Timed 25-Foot Walk (T25FW), and 9-Hole Peg Test (9HPT). The primary outcome in part 2 was the incidence of adverse events and serious adverse events. Efficacy and safety analyses were done in the intention-to-treat population. This trial is registered with ClinicalTrials.gov, number NCT01416181. Findings: Between Sept 13, 2011, and July 16, 2015, 889 patients were randomly assigned (n=440 to the natalizumab group, n=449 to the placebo group). In part 1, 195 (44%) of 439 natalizumab-treated patients and 214 (48%) of 448 placebo-treated patients had confirmed disability progression (odds ratio [OR] 0·86; 95% CI 0·66–1·13; p=0·287). No treatment effect was observed on the EDSS (OR 1·06, 95% CI 0·74–1·53; nominal p=0·753) or the T25FW (0·98, 0·74–1·30; nominal p=0·914) components of the primary outcome. However, natalizumab treatment reduced 9HPT progression (OR 0·56, 95% CI 0·40–0·80; nominal p=0·001). In part 1, 100 (22%) placebo-treated and 90 (20%) natalizumab-treated patients had serious adverse events. In part 2, 291 natalizumab-continuing patients and 274 natalizumab-naive patients received natalizumab (median follow-up 160 weeks [range 108–221]). Serious adverse events occurred in 39 (13%) patients continuing natalizumab and in 24 (9%) patients initiating natalizumab. Two deaths occurred in part 1, neither of which was considered related to study treatment. No progressive multifocal leukoencephalopathy occurred. Interpretation: Natalizumab treatment for secondary progressive multiple sclerosis did not reduce progression on the primary multicomponent disability endpoint in part 1, but it did reduce progression on its upper-limb component. Longer-term trials are needed to assess whether treatment of secondary progressive multiple sclerosis might produce benefits on additional disability components. Funding: Biogen

MAMMALS IN PORTUGAL : A data set of terrestrial, volant, and marine mammal occurrences in P ortugal

Mammals are threatened worldwide, with 26% of all species being includedin the IUCN threatened categories. This overall pattern is primarily associatedwith habitat loss or degradation, and human persecution for terrestrial mam-mals, and pollution, open net fishing, climate change, and prey depletion formarine mammals. Mammals play a key role in maintaining ecosystems func-tionality and resilience, and therefore information on their distribution is cru-cial to delineate and support conservation actions. MAMMALS INPORTUGAL is a publicly available data set compiling unpublishedgeoreferenced occurrence records of 92 terrestrial, volant, and marine mam-mals in mainland Portugal and archipelagos of the Azores and Madeira thatincludes 105,026 data entries between 1873 and 2021 (72% of the data occur-ring in 2000 and 2021). The methods used to collect the data were: live obser-vations/captures (43%), sign surveys (35%), camera trapping (16%),bioacoustics surveys (4%) and radiotracking, and inquiries that represent lessthan 1% of the records. The data set includes 13 types of records: (1) burrowsjsoil moundsjtunnel, (2) capture, (3) colony, (4) dead animaljhairjskullsjjaws, (5) genetic confirmation, (6) inquiries, (7) observation of live animal (8),observation in shelters, (9) photo trappingjvideo, (10) predators dietjpelletsjpine cones/nuts, (11) scatjtrackjditch, (12) telemetry and (13) vocalizationjecholocation. The spatial uncertainty of most records ranges between 0 and100 m (76%). Rodentia (n=31,573) has the highest number of records followedby Chiroptera (n=18,857), Carnivora (n=18,594), Lagomorpha (n=17,496),Cetartiodactyla (n=11,568) and Eulipotyphla (n=7008). The data setincludes records of species classified by the IUCN as threatened(e.g.,Oryctolagus cuniculus[n=12,159],Monachus monachus[n=1,512],andLynx pardinus[n=197]). We believe that this data set may stimulate thepublication of other European countries data sets that would certainly contrib-ute to ecology and conservation-related research, and therefore assisting onthe development of more accurate and tailored conservation managementstrategies for each species. There are no copyright restrictions; please cite thisdata paper when the data are used in publications.info:eu-repo/semantics/publishedVersio

Genome of Herbaspirillum seropedicae Strain SmR1, a Specialized Diazotrophic Endophyte of Tropical Grasses

The molecular mechanisms of plant recognition, colonization, and nutrient exchange between diazotrophic endophytes and plants are scarcely known. Herbaspirillum seropedicae is an endophytic bacterium capable of colonizing intercellular spaces of grasses such as rice and sugar cane. The genome of H. seropedicae strain SmR1 was sequenced and annotated by The Paraná State Genome Programme—GENOPAR. The genome is composed of a circular chromosome of 5,513,887 bp and contains a total of 4,804 genes. The genome sequence revealed that H. seropedicae is a highly versatile microorganism with capacity to metabolize a wide range of carbon and nitrogen sources and with possession of four distinct terminal oxidases. The genome contains a multitude of protein secretion systems, including type I, type II, type III, type V, and type VI secretion systems, and type IV pili, suggesting a high potential to interact with host plants. H. seropedicae is able to synthesize indole acetic acid as reflected by the four IAA biosynthetic pathways present. A gene coding for ACC deaminase, which may be involved in modulating the associated plant ethylene-signaling pathway, is also present. Genes for hemagglutinins/hemolysins/adhesins were found and may play a role in plant cell surface adhesion. These features may endow H. seropedicae with the ability to establish an endophytic life-style in a large number of plant species