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A deep convolutional neural network for real-time full profile analysis of big powder diffraction data

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npj Computational materials 2021年第1期7卷 671-679页

作者： Hongyang Dong Keith T.Butler Dorota matras Stephen W.T.Price Yaroslav Odarchenko Rahul Khatry Andrew Thompson Vesna middelkoop simon D.m.Jacques Andrew m.Beale Antonis Vamvakeros Department of Chemistry University College London20 Gordon StreetLondon WC1H 0AJUnited Kingdom ScimL Scientific Computer DivisionSTFCRutherford Appleton LaboratoryHarwell OX110QXUnited Kingdom Finden Limited Merchant House5 East St Helens StreetAbingdon OX145EGUnited Kingdom National Physical Laboratory Hampton RoadTeddington TW110LWUnited Kingdom Flemish Institute for Technological Research VITO NVBoeretang 200Mol 2400Belgium Research Complex at Harwell Rutherford Appleton LaboratoryHarwell Science and Innovation CampusDidcotOX110FA OxfordshireUnited Kingdom Present address:Diamond Light Source Harwell Science and Innovation CampusDidcotOxfordshire OX110DEUnited Kingdom Present address:The Faraday Institution Quad OneHarwell Science and Innovation CampusOX110RA OxfordshireUnited Kingdom

We present Parameter Quantification Network(PQ-Net),a regression deep convolutional neural network providing quantitative analysis of powder X-ray diffraction patterns from multi-phase *** network is tested against simulated and experimental datasets of increasing complexity with the last one being an X-ray diffraction computed tomography dataset of a multi-phase Ni-Pd/CeO_(2)-ZrO_(2)/Al_(2)O_(3) catalytic material system consisting of ca.20,000 diffraction *** is shown that the network predicts accurate scale factor,lattice parameter and crystallite size maps for all phases,which are comparable to those obtained through full profile analysis using the Rietveld method,also providing a reliable uncertainty measure on the *** main advantage of PQNet is its ability to yield these results orders of magnitude faster showing its potential as a tool for real-time diffraction data analysis during in situ/operando experiments.

关键词： network powder analysis

magnetotactic bacteria from the human gut microbiome associated with orientation and navigation regions of the brain

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Journal of Oceanology and Limnology 2021年第6期39卷 2044-2052页

作者： Rozalyn A.simon Purnika Damindi RANASINGHE Nawroz BARAZANJI malin Bergman JUNGESTRÖm Jie XU Olga BEDNARSKA Lena SERRANDER maria ENGSTRÖm Dennis A.BAZYLINSKI Åsa V.KEITA Susanna WALTER Center for medical Image Science and Visualization(CmIV) Linköping UniversityLinköping 58183Sweden Department of Health Medicineand Caring SciencesLinköping UniversityLinköping 58183Sweden Division of Infection and Infl ammation Department of Biomedical and Clinical SciencesLinköping UniversityLinköping 58183Sweden Institute of Global Food Security School of Biological SciencesQueen’s University BelfastBelfast BT95DLUnited Kingdom School of Life Sciences University of Nevada at Las VegasLas VegasNevada 89154USA Division of Surgery Orthopedics and OncologyDepartment of Clinical and Experimental MedicineLinköping UniversityLinköping 58183Sweden

magnetotactic bacteria(mTB),ubiquitous in soil and fresh and saltwater sources have been identified in the microbiome of humans and many *** endogenously produce magnetic nanocrystals enabling them to orient and navigate along geomagnetic *** magnetite deposits have been found throughout the tissues of the human brain,including brain regions associated with orientation such as the cerebellum and hippocampus,the origins of which remain *** over the role and source of mTB in humans,as well as any association with the brain,remain *** performed a metagenomic analysis of the gut microbiome of 34 healthy females as well as grey matter volume analysis in magnetite-rich brain regions associated with orientation and navigation with the goal of identifying specific mTB that could be associated with brain structure in orientation and navigation *** identified seven mTB in the human gut microbiome:magnetococcus marinus,magnetospira ***-2,magnetospirillum magneticum,magnetospirillum ***-1,magnetospirillum ***-1,magnetospirillum gryphiswaldense,and Desulfovibrio *** preliminary results show significant negative associations between multiple mTB with bilateral flocculonodular lobes of the cerebellum and hippocampus(adjusted for total intracranial volume,uncorrected PmTB in the gut are associated with grey matter volume in magnetite-rich brain regions related to orientation and *** preliminary findings support mTB as a potential biogenic source for brain magnetite in *** studies will be necessary to validate and elucidate the relationship between these bacteria,magnetite concentrations,and brain function.

关键词： magnetotactic bacteria human microbiome microbiota-gut-brain axis magnetoreception

A Specific Class of Short Treadmilling microtubules Enhances Cortical microtubule Alignment

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molecular Plant 2016年第8期9卷 1214-1216页

作者： Guillaume Chomicki Raymond Wightman simon R. Turner Faculty of Life Sciences University of Manchester Oxford Road Manchester M13 9PT UK

Dear Editor Anisotropic cell expansion is a property of plant cells that is dependent upon the formation of a highly ordered cortical micro- tubule （mT） array. The orientation of cortical microtubules is crit- ical for guiding cellulose synthase complexes in the plasma mem- brane and thereby determining the direction of the cell expansion （Paredez et al., 2006）.

关键词： dependent thereby direction

Potential for natural and enhanced attenuation of sulphanilamide in a contaminated chalk aquifer

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Journal of Environmental Sciences 2017年第12期29卷 39-48页

作者： Karen A.Bennett simon D.Kelly Xiangyu Tang Brian J.Reid School of Environmental Sciences University of East AngliaNorwich Research ParkNorwich NR4 7TJUK Food and Environmental Protection Laboratory International Atomic Energy Agency1400 ViennaAustria Key Laboratory of mountain Surface Processes and Ecological Regulation Institute of Mountain Hazards and EnvironmentChinese Academyof SciencesChengdu 610041China

Understanding antibiotic biodegradation is important to the appreciation of their fate and removal from the environment. In this research an Isotope Ratio mass Spectrometry（IRmS）method was developed to evaluate the extent of biodegradation of the antibiotic,sulphanilamide, in contaminated groundwater. Results indicted an enrichment in δ^（13）C of8.44‰ from-26.56（at the contaminant source） to-18.12‰（300 m downfield of the source）.These results confirm reductions in sulphanilamide concentrations（from 650 to 10 mg/L）across the contaminant plume to be attributable to biodegradation（56%） vs. other natural attenuation processes, such as dilution or dispersion（42%）. To understand the controls on sulphanilamide degradation ex-situ microcosms assessed the influence of sulphanilamide concentration, redox conditions and an alternative carbon source. Results indicated, high levels of anaerobic capacity（~50% mineralisation） to degrade sulphanilamide under high（263 mg/L）, moderate（10 mg/L） and low（0.02 mg/L） substrate concentrations. The addition of electron acceptors; nitrate and sulphate, did not significantly enhance the capacity of the groundwater to anaerobically biodegrade sulphanilamide. Interestingly, where alternative carbon sources were present, the addition of nitrate and sulphate inhibited sulphanilamide biodegradation. These results suggest, under in-situ conditions, when a preferential carbon source was available for biodegradation, sulphanilamide could be acting as a nitrogen and/or sulphur source. These findings are important as they highlight sulphanilamide being used as a carbon and a putative nitrogen and sulphur source, under prevailing iron reducing conditions.

关键词： Antibiotics Sulphonamide Groundwater contamination Biodegradation Stable isotope fractionation IRmS

Plasticity of Xyloglucan Composition in Bean （Phaseolus vulgaris）-Cultured Cells during Habituation and Dehabituation to Lethal Concentrations of Dichlobenil

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molecular Plant 2010年第3期3卷 603-609页

作者： A. Alonso-simon L. Neumetzler R Garcia-Angulo A.E. Encina J.L. Acebes J.m. Alvarez T. Hayashi Area de Fisiologia Vegetal Universidad de Leon E-24071 Leon Spain max Planck Institute of molecular Plant Physiology 14476 Golm Germany Kyoto University RISH Gokasho Uji Kyoto 611-0011 Japan

Bean cells that have been habituated to grow in a lethal concentration （12 μm） of 2,6-dichlorobenzonitrile （dichlobenil or DCB, a cellulose biosynthesis inhibitor） are known to have decreased cellulose content in their cell walls. Xyloglucan, which is bound to cellulose and together with it forms the main loading network of plant cell walls, has also been described to decrease in habituated cells, but whether the change on cellulose affects the xyloglucan structure besides its abundance has not been analyzed. Fragmentation analysis with xyloglucan-specific endoglucanase （XEG） and endocellulase revealed that habituation to DCB caused a change in the fine structure of xyloglucan, namely a decrease in fucosyl residues attached to the galactosyl-xylosyl residues along the glucan backbone. After the removal of herbicide from the medium （dehabituated cells）, xyloglucan recovered its fucosyl residues. In addition, some cello-oligosaccharides could be detected only in habituated cells＇ xyloglucan digested by XEG and endocellulase, corresponding to a glucan co- valently bound or co-precipitated with the hemicelluloses. These results show that structural flexibility of cell walls relies in part on the plasticity of xyloglucan composition and opens up new perspectives to further research in this field.

关键词： Bean 2,6-dichlorobenzonitrile habituation and dehabituation OLImP (Oligosaccharides mass Profiling) xyloglucan.

mass Screening Using Antigenic and molecular Diagnostic Tests of COVID-19 in Bangui at the Beginning of the Second Wave in July 2021

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Journal of Tuberculosis Research 2024年第1期12卷 1-12页

作者： Clotaire Donatien Rafaï marie-Roseline Darnycka Belizaire Pierre Somse Wilfrid Sylvain Nambei Ernest Lango-Yaya Oscar Senzongo Luc Salva Hereidebona Ulrich Jeffrey Kotemossoua Rabbi mermoz Senekian simon Pounguinza Christian-Diamant mossoro-Kpinde Alain Le Faou Jean De Dieu Longo François-Xavier mbopi-Keou Gérard Grésenguet Boniface Koffi National Laboratory of Clinical Biology and Public Health Bangui Central African Republic Faculty of Health Sciences University of Bangui Bangui Central African Republic World Health Organization Bangui Central African Republic ministry of Health and Population Bangui Central African Republic Faculty of medicine Maieutic and Health Sciences University of Lorraine Pole Brabois Santé Nancy France Faculty of medicine and Biomedical Sciences University of Yaounde I Yaounde Cameroun

Objective: COVID-19 surveillance was established as early as march 2020 in the Central African Republic (CAR), after the WHO statement relating to the identification of several cases outside China. However, given the non-performing molecular biology technical platform in many developing countries in sub-Saharan Africa, the second wave promised to be surprising and formidable. In this context, a mass survey was launched in Bangui to determine the prevalence of COVID-19. Patients and methods: From march 18 to April 2, 2021, a mass screening campaign took place in tourist places, companies and the main hospital infrastructures. Nasopharyngeal swab samples were collected from participants with and without symptoms of Influenza-like illness (ILI) and stored in VTm tubes. The Ag (COVID-19) and RT-PCR tests were carried out in Bangui at the LNBCSP. The sequencing of RT-PCR SARS-CoV-2 positives was carried out at the INRB. Results: We included 1480 participants of whom 33 (2.23%) were SARS-COV-2 positive, of whom 24 were male and 9 female. This sex difference was statistically significant (p = 0.012) as the sex ratio m/F was 1.09. Sampling sites located in the 1st arrondissement were the most prolific (p = 0.006) and were sequenced. In addition to the analysis of the 33 samples from the predefined sites under study, 17 control sequences from the provinces generated during the same period are added. We detected 2 Variants Of Concern (VOC) including the predominant B.1.620 (43.86%) followed by B.1.1.7 or Alpha (5.10%). Conclusion: The study showed the importance of surveillance and the availability of means of diagnosis of COVID-19. The identified risk factors were sex and sampling site. This study has shown the importance of setting up sentinel sites for COVID-19 surveillance in all regions of the country and the appropriate use of the anti-COVID-19 vaccine.

关键词： COVID-19 Variants Central African Republic

A systematic review and meta-analysis to determine the effect of sperm DNA damage on in vitro fertilization and intracytoplasmic sperm injection outcome

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Asian Journal of Andrology 2017年第1期19卷 80-90页

作者： Luke simon Armand Zini Alina Dyachenko Antonio Ciampi Douglas T Carrell Department of Surgery (Urology) University of Utah School of Medicine Salt Lake City UT USA Division of Urology Department of Surgery St. Mary's Hospital Center St. Mary's Hospital 3830 Lacombe Avenue Montreal Quebec H3T 1M5 Canada Department of Human Genetics University of Utah School of Medicine Salt Lake City UT USA Department of Obstetrics and Gynecology University of Utah School of Medicine Salt Lake City UT USA.

Sperm DNA damage is prevalent among infertile men and is known to influence natural reproduction. However, the impact of sperm DNA damage on assisted reproduction outcomes remains controversial. Here, we conducted a meta-analysis of studies on sperm DNA damage （assessed by SCSA, TUNEL, SCD, or Comet assay） and clinical pregnancy after IVF and/or ICSI treatment from mEDLINE, EmBASE, and PUBmED database searches for this analysis. We identified 41 articles （with a total of 56 studies） including 16 IVF studies, 24 ICSI studies, and 16 mixed （IVF ＋ ICSI） studies. These studies measured DNA damage （by one of four assays： 23 SCSA, 18 TUNEL, 8 SCD, and 7 Comet） and included a total of 8068 treatment cycles （3734 IVF, 2282 ICSI, and 2052 mixed IVF ＋ ICSI）. The combined OR of 1.68 （95% Ch 1.49-1.89; P 〈 0.0001） indicates that sperm DNA damage affects clinical pregnancy following IVF and/or ICSI treatment. In addition, the combined OR estimates of IVF （16 estimates, OR = 1.65; 95% CI： 1.34-2.04; P 〈 0.0001）, ICSI （24 estimates, OR = 1.31; 95% Ch 1.08-1.59; P = 0.0068）, and mixed IVF ＋ ICSI studies （16 estimates, OR = 2.37; 95% Ch 1.89-2.97; P〈 0.0001） were also statistically significant. There is sufficient evidence in the existing literature suggesting that sperm DNA damage has a negative effect on clinical pregnancy following IVF and/or ICSI treatment.

关键词： assisted reproductive technology outcomes clinical pregnancy meta-analysis sperm DNA damage systematic review

The association between sexual function and prostate cancer risk in US veterans

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Asian Journal of Andrology 2017年第2期19卷 191-195页

作者： Daniel F Zapata Lauren E Howard Jennifer Frank Ross m simon Cathrine Hoyo Delores J Grant Stephen J Freedland Adriana C Vidal Duke University medical Center Division of Urology Department of Surgery Durham NC 27710 USA Durham Veterans Affairs medical Center Urology Division Durham NC 27710 USA North Carolina State University Department of Biology Raleigh NC 27695 USA North Carolina Central University Department of Biology Durham NC 27707 USA Department of Surgery Division of Urology Samuel Oschin Comprehensive Cancer institute Cedars-Sinai Medical Center Los Angeles California 90048 USA

Sexual dysfunction and prostate cancer are common among older men. Few studies explored the association between these two illnesses. We examined whether sexual function is associated with prostate cancer risk among older men. Among 448 men undergoing prostate biopsy at the Durham Veterans Affairs Hospital, sexual function was ascertained from the Expanded Prostate Cancer Index Composite sexual assessment. We tested the link between sexual function and prostate cancer risk adjusting for multiple demographic and clinical characteristics using logistic regression. multinomial logistic regression was used to test the associations with risk of low-grade （Gleason 〈6） and high-grade （Gleason 〉7 or 〉4 ＋ 3） disease versus no cancer. Of 448 men, 209 （47%） had a positive biopsy; these men were less likely to be white （43% vs 55%, P=0.013）, had higher prostate-specific antigen （PSA）（6.0 vs 5.4 ng ml-1, P 〈 0.001）, but with lower mean sexual function score （47 vs 54, P = 0.007）. There was no difference in age, BmI, pack years smoked, history of heart disease and/or diabetes. After adjusting for baseline differences, sexual function was linked with a decreased risk of overall prostate cancer risk （OR. 0.91 per lO-point change in sexual function, P= 0.004） and high-grade disease whether defined as Gleason ≥7 （OR： 0.86, P= 0.001） or 〉4 ＋ 3 （OR： 0.85, P= 0.009）. Sexual function was unrelated to low-grade prostate cancer （OR： 0.94, P = 0.13）. Thus, among men undergoing prostate biopsy, higher sexual function was associated with a decreased risk of overall and high-grade prostate cancer. Confirmatory studies are needed.

关键词： erectile dysfunction prostate prostate cancer risk sexual function

The anti-obesity effects of EGCG in relation to oxidative stress and air-pollution in China

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Natural Products and Bioprospecting 2013年第6期3卷 256-266页

作者： simon CICHELLO Pingsheng LIU markendya JOIS School of Life Sciences La Trobe UniversityVictoria 3086Australia National Laboratory of Biomacromolecules Institute of BiophysicsChinese Academy of SciencesBeijing 100101China ministry of Education Key Laboratory of Pu'er Tea Yunnan Agricultural UniversityYunnan 650201China

modern China,similar to most developing nations,has seen a rise in the prevalence of both obesity and diesel exhaust based air *** cause of obesity is multi-factorial encompassing diet,lifestyle and social *** there has been a reduction in the consumption of fruit,vegetables,and traditional medicinal foods such as polyphenol containing green *** these,are high fat and carbohydrate based processed foods which are quickly displacing these wholefoods in the *** review paper proposes evidence that a potential cause of obesity is also linked to environmental stress stimuli such as air pollutants,particularly diesel exhaust fumes(DEF)of>2.5μm particulate matter,and discusses a role for a green tea catechin(EGCG)for use as a dietary defence against diet and environmentally induced *** is now at a critical point of a public health pandemic with rising air-borne pollution(via car exhaust fumes DEF),industry pollution such as heavy metals,and the benzene hydrocarbon based‘2Pm’particulate matter,now accepted as a major environmental issue for public *** data published in mEDLINE since 1995 has been gathered to formulate the following review.

关键词： EGCG obesity air-pollution diesel exhaust fumes(DEF) 2Pm reactive oxygen species(ROS) inflammation