bluuebunny/crossref_metadata_2025 huggingface dataset:
Optimal cut points of N-terminal of the prohormone brain natriuretic peptide (NT-proBNP) in patients with COVID-19
Authors: Chehrazi Mohammad , Yavarpour Hanieh , Jalali Farzad , Saravi Mehrdad , Jafaripour Iraj , Hedayati Mohammad Taghi , Amin Kamyar , Pourkia Roghayeh , Abroutan Saied , Javanian Mostafa , Ebrahimpour Soheil , Ziaie Naghmeh
Published: March 2022

Background

COVID19 patients may suffer from multiple cardiovascular complications. Recently, N-terminal of the prohormone brain natriuretic peptide (NT-proBNP) was a potentially independent risk factor for COVID-19 in-hospital death. The present study aimed to find new optimal cut points for NT-proBNP across censored survival failure time outcomes in hospitalized COVID-19 patients.

Results

This cohort study was conducted on 272 patients with COVID-19 whose initial records were recorded from March 2020 to July 2020. Demographic characteristics, clinical examinations, and laboratory measurements were collected at the beginning of the admission registered in the patient record system located in the hospital. We used the maximally selected rank statistics to determine the optimal cut points for NT-proBNP (the most significant split based on the standardized log-rank test). Survival time was defined as the days from hospital admission to discharge day. In this cohort study, two optimal cut points for NT-proBNP were 331 (pg/mL) and 11,126 (pg/mL) based on a survival model. The adjusted HR of NT-proBNP for in-hospital death was 3.41 (95% CI: 1.22–9.51, P = 0.02) for medium against low category, and 3.84 (95% CI: 1.30–11.57, P = 0.01) for high in comparison with low group.

Conclusions

We reported a dramatically increased concentration of NT-proBNP among COVID-19 patients without heart failure in both severe and non-severe cases. Moreover, our study showed that a high level of NT-proBNP was highly associated with the prolonged survival time of patients with COVID-19. NT-proBNP is a strong prognostic indicator of in-hospital death in the second week of admission.
Tailoring enhanced production and identification of isoflavones in the callus cultures of Pueraria thomsonii Benth and its model verification using response surface methodology (RSM): a combined in vitro and statistical optimization
Authors: Li Yu , Saravana Kumar Pachaiyappan , Liu Yu , Qiu Jiao , Ran Yalan , Yuan Mingyuan , Fang Xinyue , Tan Xuhui , Zhao Renjun , zhu Ji , He Meijun
Published: March 2022

Background

Scientifically, isoflavones from Pueraria thomsonii Benth possess diverse pharmacological activities and have been used to treat various diseases. In vitro propagation of callus has contributed to the reliability for large-scale production of target compounds. However, the factors affecting the biosynthesis of major isoflavones daidzin, puerarin and daidzein in the callus culture of P. thomsonii are still not known. Therefore, we aimed to enhance the in vitro production of daidzin, puerarin and daidzein by optimizing three independent factors such as temperature, NAA and 6-BA concentrations.

Results

Our findings showed that the optimal concentrations for in vitro biomass production and efficient synthesis of puerarin, daidzin and daidzein were found to be 0.158%, 0.463% and 0.057%, respectively. In addition, the HPLC fingerprint with chemo-metrics analysis was constructed by linear regression of the puerarin, daidzin and daidzein which was found to be in the range of 1.0–36.0, 5.0–72.0 and 1.0–15.0 mg/mL and the LODs and LOQs were found to be 0.15, 0.52, 0.35 and 0.28, 1.50, 0.50 mg/mL for puerarin, daidzin and daidzein, respectively. Surprisingly, our results were also in agreement with the concentration obtained from the model verification for optimal and efficient production of puerarin, daidzin and daidzein which was found to be 0.162%, 0.458% and 0.049%, respectively.

Conclusions

In summary, our present investigation provides new insights that could facilitate the enhanced production of valuable isoflavones in P. thomsonii using plant cell cultures treated with appropriate elicitor combinations and temperature. As far as the authors are concerned, this is the first report on production of daidzin, puerarin and daidzein at higher yield at laboratory level for a wide range of applications in future food, medicinal and pharmaceutical companies.
Personal, social, and environmental correlates of physical activity and sport participation in an adolescent Turkish population
Authors: Timurtaş Eren , Selçuk Halit , Çınar Eda , Demirbüken İlkşan , Sertbaş Yaşar , Polat Mine Gülden
Published: March 2022

Background

Benefits of physical activity has been shown for adolescents; however, there is a decline trend in number of adolescents meeting current WHO recommendations. This trend underlines the importance of identifying factors associated with adolescents’ physical activity level (PAL) with considerations of regional and cultural differences to plan and implement effective policies. Therefore, the aim of this study was to determine personal, ecological, and social factors associated with PAL and sport participation in Turkish adolescents aged 11–14 years. A cross-sectional study was conducted by including 996 adolescents aged between 11 and 14 years from 39 secondary schools in İstanbul, Turkey. Logistic regression analyses performed to identify the significant personal (age, gender, sleep time, screen time, BMIz score, having siblings), ecological (presence of playground, type of school transportation), and social (family income, engaging a physical activity with family, and preferred activity at school breaks) predictors of PAL and sport participation.

Results

Adolescents who were active during break time at school (p< 0.001), engaging a physical activity with family (p< 0.001), and did not have a sibling (p= 0.029) were more likely to be physically active. Adolescents behaved active during break time at school (p< 0.001), had a playground at home (p< 0.001), spending time with family for physical activity (p< 0.001), and did not have a sibling (p= 0.021) were more likely to participate in a sport activity.

Conclusions

Predictors of PAL in this study indicates the need to promote active break time in school, increased physical activity time with family, and to design environmental policies to increase number of playgrounds.
The Experiences of Undergraduates with Depression in Online Science Learning Environments
Authors: Mohammed Tasneem F. , Gin Logan E. , Wiesenthal Nicholas J. , Cooper Katelyn M.
Published: March 2022

This interview study of 24 undergraduates with depression examined how depression affects student cognitive domains when learning science online and how aspects of online science courses affect student depression. The study yielded recommendations about how to create inclusive online science courses for students with depression.
Clinical Research Professional Providing Care Coordination Support: A Study of Hawaii Minority/Underserved NCORP Community Site Trial Participants
Authors: Okado Izumi , Pagano Ian , Cassel Kevin , Su'esu'e Anamalia , Rhee Jessica , Berenberg Jeffrey , Holcombe Randall F.
Published: March 2022

PURPOSE:

Although effective care coordination (CC) is recognized as a vital component of a patient-centered, high-quality cancer care delivery system, CC experiences of patients who enroll and receive treatment through clinical trials (CTs) are relatively unknown. Using mixed methods, we examined perceptions of CC among patients enrolled onto therapeutic CTs through the Hawaii Minority/Underserved National Cancer Institute Community Oncology Research Program.

METHODS:

The Care Coordination Instrument, a validated instrument, was used to measure patients' perceptions of CC among CT participants (n = 45) and matched controls (n = 45). Paired t-tests were used to compare overall and three CC domain scores (Communication, Navigation, and Operational) between the groups. Semistructured focus group interviews were conducted virtually with 14 CT participants in 2020/2021.

RESULTS:

CT participants reported significantly higher total CC scores than non-CT participants ( P = .0008). Similar trends were found for Navigation and Operational domain scores ( P = .007 and .001, respectively). Twenty-nine percent of CT participants reported receiving high-intensity CC assistance from their clinical research professionals (CRPs). Content analysis of focus group discussions revealed that nearly half of the focus group discussions centered on CRPs (47%), including CC support provided by CRPs (26%). Other key themes included general CT experiences (22%) and CRP involvement as an additional benefit to CT participation (15%).

CONCLUSION:

Our results show that patients on CTs in this study had a more positive CC experience. This may be attributable in part to CC support provided by CRPs. These findings highlight both the improved experience of treatment for patients participating in a trial and the generally unrecognized yet integral role of CRPs as part of a cancer CT care team.
Changes in Triple-Negative Breast Cancer Molecular Subtypes in Patients Without Pathologic Complete Response After Neoadjuvant Systemic Chemotherapy
Authors: Masuda Hiroko , Harano Kenichi , Miura Sakiko , Wang Ying , Hirota Yuko , Harada Oi , Jolly Mohit Kumar , Matsunaga Yuki , Lim Bora , Wood Anita L. , Parinyanitikul Napa , Jin Lee Hee , Gong Gyungyub , George Jason T. , Levine Herbert , Lee Jangsoon , Wang Xiaoping , Lucci Anthony , Rao Arvind , Schweitzer Brock L. , Lawrence O. Rayne , Seitz Robert S. , Morris Stephan W. , Hout David R. , Nakamura Seigo , Krishnamurthy Savitri , Ueno Naoto T.
Published: March 2022

PURPOSE

Lehmann et al have identified four molecular subtypes of triple-negative breast cancer (TNBC)—basal-like (BL) 1, BL2, mesenchymal (M), and luminal androgen receptor—and an immunomodulatory (IM) gene expression signature modifier. Our group previously showed that the response of TNBC to neoadjuvant systemic chemotherapy (NST) differs by molecular subtype, but whether NST affects the subtype was unknown. Here, we tested the hypothesis that in patients without pathologic complete response, TNBC subtypes can change after NST. Moreover, in cases with the changed subtype, we determined whether epithelial-to-mesenchymal transition (EMT) had occurred.

MATERIALS AND METHODS

From the Pan-Pacific TNBC Consortium data set containing TNBC patient samples from four countries, we examined 64 formalin-fixed, paraffin-embedded pairs of matched pre- and post-NST tumor samples. The TNBC subtype was determined using the TNBCtype-IM assay. We analyzed a partial EMT gene expression scoring metric using mRNA data.

RESULTS

Of the 64 matched pairs, 36 (56%) showed a change in the TNBC subtype after NST. The most frequent change was from BL1 to M subtypes (38%). No tumors changed from M to BL1. The IM signature was positive in 14 (22%) patients before NST and eight (12.5%) patients after NST. The EMT score increased after NST in 28 (78%) of the 36 patients with the changed subtype ( v 39% of the 28 patients without change; P = .002254).

CONCLUSION

We report, to our knowledge, for the first time that the TNBC molecular subtype and IM signature frequently change after NST. Our results also suggest that EMT is promoted by NST. Our findings may lead to innovative adjuvant therapy strategies in TNBC cases with residual tumor after NST.
SCARECROW is deployed in distinct contexts during rice and maize leaf development
Authors: Hughes Thomas E. , Langdale Jane A.
Published: March 2022

The flexible deployment of developmental regulators is an increasingly appreciated aspect of plant development and evolution. The GRAS transcription factor SCARECROW (SCR) regulates the development of the endodermis in Arabidopsis and maize roots, but during leaf development it regulates the development of distinct cell types; bundle-sheath in Arabidopsis and mesophyll in maize. In rice, SCR is implicated in stomatal patterning, but it is unknown whether this function is additional to a role in inner leaf patterning. Here, we demonstrate that two duplicated SCR genes function redundantly in rice. Contrary to previous reports, we show that these genes are necessary for stomatal development, with stomata virtually absent from leaves that are initiated after germination of mutants. The stomatal regulator OsMUTE is downregulated in Osscr1;Osscr2 mutants, indicating that OsSCR acts early in stomatal development. Notably, Osscr1;Osscr2 mutants do not exhibit the inner leaf patterning perturbations seen in Zmscr1;Zmscr1h mutants, and Zmscr1;Zmscr1h mutants do not exhibit major perturbations in stomatal patterning. Taken together, these results indicate that SCR was deployed in different developmental contexts after the divergence of rice and maize around 50 million years ago.
Syntaxonomy and ecology of thermophilous deciduous open woodlands and scrub vegetation in Tajikistan (Middle Asia)
Authors: Nowak Arkadiusz , Nobis Marcin , Nowak Sylwia , Kotowski Marcin , Klichowska Ewelina , Nobis Agnieszka , Świerszcz Sebastian
Published: March 2022

In this paper we present the first syntaxonomic classification for the thermophilous open wood and scrub vegetation in Tajikistan with some remarks on its environmental gradients. Altogether 143 relevés were sampled between 2014–2021 using the seven-degree cover-abundance scale of Braun-Blanquet. They were classified by the modified TWINSPAN method with the use of the four step interval scale with cutoff levels of 0%, 2%, 5% and 10% and total inertia as a measure of cluster heterogeneity. Diagnostic species were identified using the phi coefficient as a fidelity measure. Detrended Correspondence Analysis was used to determine the relation between samples, vegetation units and the major gradients in species composition. Plant communities have been divided into three main groups: (1) dry scrub on screes, (2) mesophilous scrubs in nemoral zone, and (3) open woods. A new class of Pistacietea khinjuki-verae has been proposed for open woods. Further classification of vegetation data resulted in the distinction of four plant communities within two provisional alliances: Roseion kokanicae and Ranunculo tenuilobi-Cotoneasterion hissaricae (commu­nities of Rosa kokanica and R. ecae, associations of Aveno ludovicianae-Rhuidetum coriariae and Calophacetum grandiflorae). Additionally, we established the Pistacion verae alliance for the pistachio groves of Middle Asia with two subassociations: Pistacietum verae typicum and Pistacietum verae cercidetosum griffithii. The main fac­tors determining the species composition of the studied communities are: elevation, temperature, precipi­tation, slope and aspect. Our research showed that the Pistacia groves are a distinct vegetation typical of the Irano-Turanian area and that further surveys are needed to present a final classification of scrub vegetation of Tajikistan.
Επικλήσεις προς το θείο και θεϊκές επιφάνειες σε τρεις ποιήτριες της Ιταλικής Αναγέννησης
Authors: Γρίβα Άννα
Published: March 2022

Η διατριβή επιχειρεί μια συγκριτική μελέτη της σαπφικής ποίησης με το έργο τριών Ιταλίδων ποιητριών της Αναγέννησης: της Gaspara Stampa (1523-1554), της Laura Battiferra (1523-1589) και της Sara Copia Sullam (1592-1641). Στο πρώτο μέρος εξετάζονται οι επικλήσεις προς το θείο και οι θεϊκές επιφάνειες στη σαπφική ποίηση ως στοιχεία κομβικά για την κατανόηση των σωζόμενων σπαραγμάτων. Στο δεύτερο μέρος γίνεται μια προσπάθεια να συναναγνωστούν οι σαπφικοί στίχοι με το έργο των τριών Ιταλίδων ποιητριών. Μέσα σε αυτό το πλαίσιο μελέτης καταγράφονται διαφορετικές μορφές πρόσληψης του σαπφικού έργου, που αφορούν επιδράσεις, απηχήσεις, κοινούς τόπους και αντικατοπτρισμούς. Έτσι, αναδεικνύεται ο τρόπος με τον οποίο η γυναίκα δημιουργός τίθεται ξανά στο προσκήνιο και συγκροτεί το δικό της κοσμοείδωλο, ξαναβρίσκοντας έναν ρόλο που είχε στερηθεί από τα αρχαία χρόνια. Συγχρόνως αναφαίνεται η επανένταξη του θείου στον κόσμο με έναν τρόπο που παρουσιάζει πολλά κοινά χαρακτηριστικά με τις αρχαιοελληνικές αντιλήψεις περί θεών και ο κεντρικός ρόλος των γυναικών δημιουργών ως μεσολαβητών του ανθρώπου με τις υπερβατικές δυνάμεις.
Building community and public engagement in research – the experience of early career researchers in East Africa
Authors: Bargul Joel L. , Mkwashapi Denna M. , Namagembe Imelda , Nakityo Immaculate , Nakimuli Annettee , Byamugisha Josaphat , Semakula Daniel , Seeley Janet , Sewankambo Nelson K.
Published: March 2022

Background: In this paper, we explain how three early career researchers actively engaged community members in health research in Kenya, Tanzania and Uganda in their research projects, and what was learnt from the experience. The research project in Kenya was on camel trypanosomiasis and the role of camel biting keds (or louse flies) in disease transmission. The project in Tanzania looked at the effect of human immunodeficiency virus (HIV) and antiretroviral therapy on fertility and ascertained the trends in the use of family planning services amongst women of reproductive age. The focus of the project in Uganda was the implementation of maternal death surveillance and the response policy to determine the cause of maternal deaths and how they might be prevented.

Methods: In the three different settings, efforts to ensure local community engagement provided a focus for the researchers to hone their skills in explaining research concepts and working in partnership with community members to co-develop ideas, their research methods and outputs.

Results: Involvement of communities in scientific research, which entailed a two-way mutual engagement process, led to (i) generation of new research ideas that shaped the work, (ii) strengthened mutual trust, and (iii) promoted uptake of research findings.

Conclusions: Our key findings strongly support the need for considering community engagement as one of the key components in research studies.
Systemic and Mucosal Concentrations of Nine Cytokines Among Individuals with Neisseria gonorrhoeae infection in Nairobi Kenya
Authors: Maina Anne , Mureithi Marianne , Kiiru John , Revathi Gunturu
Published: March 2022

Introduction The human-restricted sexually transmitted Neisseria gonorrhoeae (NG) has been shown to modulate the immune response against it and consequently the cytokines produced. The levels of cytokines in NG infection in the African population have not been well described. We aimed to quantify the systemic and mucosal cytokines in NG infection.

Methods This was a comparative cross-sectional study. Levels of nine cytokines (IL-1b, IL-2, IL-4, 1L-6, 1L-10, 1L-12p70, IL-17A, TNF-a and INF-g) were measured from plasma and genital samples (urethral swabs in men and cervicovaginal lavage in women) from 61 Neisseria gonorrhoeae infected individuals seeking treatment for sexually transmitted infections (STIs) at Casino Health Centre in Nairobi, Kenya. A comparative group of 61 NG-uninfected individuals, seeking treatment at the same facility but with laboratory-confirmed negative Neisseria gonorrhoeae, Chlamydia trachomatis (CT), Mycoplasma genitalium (MG) and Trichomonas vaginalis(TV) was also included. The Mann-Whitney U test was used to compare the cytokine levels between NG-infected and uninfected individuals. Data was analyzed using STATA ver. 15.1.

Results Overall, systemic IL-6, TNF-a and IL-10 were elevated while genital IL-10 and TNF-a were lower in NG positive participants. On subgroup analysis by sex, the levels of genital IL-1b and IL-6 and systemic IL-6 were elevated in NG-infected men. None of the genital cytokines were elevated in NG-infected women, while all systemic cytokines, except INF-g, were elevated in NG-infected women.

Conclusion  Neisseria gonorrhoeae induced the production of different cytokines in men and women, with men having a pro-inflammatory genital response. These differences should be taken into consideration during development of various interventions e.g. vaccine development.
Prevalence of oral manifestations in patients with lupus erythematosus in a sample of the Egyptian population: a hospital based cross-sectional study
Authors: Saeed Hager Moustafa , Mohammad Amr Eman , Rezk Lotfy Rezk Alshaimaa , Abd Elmoneim Wesam
Published: March 2022

Background: Several systemic diseases manifest themselves in the oral cavity. Dentists who are unaware of these lesions will possibly miss them. This cross-sectional study aimed to assess the prevalence of oral manifestations in patients with LE in a sample of the Egyptian population.

Methods: A descriptive study was performed on 189 patients attending the Internal Medicine Department, Rheumatology Clinic in EL Qasr EL Ainy Hospital, Cairo University. Every patient was examined clinically after completing a questionnaire. Moreover, patients’ medical records were also evaluated.  The oral manifestations were recorded according to the WHO guide to physical examination of the oral cavity and classified according to their morphologic aspects and localization.

Results: Out of 189 patients, there were 182 females (96.3%) and seven males (3.7%). The prevalence of oral lesions in SLE patients was 55.6%. The most affected site was the tongue 25.7%. The most common clinical aspect was patches, 53%. About 77.1% of the lesions were asymptomatic. 

Conclusions: The present study emphasizes the importance of early diagnosis of oral lesions to recognize patients with SLE as the WHO considers oral manifestations of SLE a widespread state. Also, implementation of oral hygiene measures and treatment to improve patients’ nutritional state and health-related quality of life are recommended.
Study protocol for the St James's Hospital, Tallaght University Hospital, Trinity College Dublin Allied Researchers' (STTAR) Bioresource for COVID-19
Authors: O'Doherty Laura , Hendricken Phelan Stuart , Wood Nicole , O'Brien Sorcha , Sui Jacklyn , Mangan Cian , Howley Fergal , O'Regan Siobhan , Razif Noor Adeebah Mohamed , Conlan Ciara , Argue Ruth , Holohan Samuel , Dyer Adam , Salleh Fara , Townsend Liam , Hughes Gerard , Kerr Colm , Reidy Derval , Sanz Alberto , Connolly Emma , Kelly Andrea , Leacy Emma , Reddy Conor , Gargan Siobhan , Breen Eamon , Hawerkamp Heike , Dunne Jean , Martin-Loeches Ignacio , McLaughlin Anne Marie , Long Aideen , Shiels Orla , Fallon Padraic , Hennessy Martina , Romero-Ortuno Roman , Bannan Ciaran , Prior Anna Rose , Rakovac Ana , McCormack William , McManus Ross , Donnelly Seamus , Bergin Colm , Little Mark , Ní Cheallaigh Clíona , Conlon Niall
Published: March 2022

Background: The current coronavirus disease 2019 (COVID-19) pandemic began in Ireland with the first confirmed positive case in March 2020. In the early stages of the pandemic clinicians and researchers in two affiliated Dublin hospitals identified the need for a COVID-19 biobanking initiative to support and enhance research into the disease. Through large scale analysis of clinical, regional, and genetic characteristics of COVID-19 patients, biobanks have helped identify, and so protect, at risk patient groups The STTAR Bioresource has been created to collect and store data and linked biological samples from patients with SARS-CoV-2 infection and healthy and disease controls.

Aim: The primary objective of this study is to build a biobank, to understand the clinical characteristics and natural history of COVID-19 infection with the long-term goal of research into improved disease understanding, diagnostic tests and treatments.

Methods: This is a prospective dual-site cohort study across two tertiary acute university teaching hospitals. Patients are recruited from inpatient wards or outpatient clinics. Patients with confirmed COVID-19 infection as well as healthy and specific disease control groups are recruited.  Biological samples are collected and a case report form detailing demographic and medical background is entered into the bespoke secure online Dendrite database.

Impact: The results of this study will be used to inform national and international strategy on health service provision and disease management related to COVID-19. In common with other biobanks, study end points  evolve over time as new research questions emerge. They currently include patient survival, occurrence of severe complications of the disease or its therapy, occurrence of persistent symptoms following recovery from the acute illness and vaccine responses.
Properties of biomass powders resulting from the fine comminution of lignocellulosic feedstocks by three types of ball-mill set-up
Authors: Rajaonarivony Rova Karine , Rouau Xavier , Fabre Charlène , Mayer-Laigle Claire
Published: March 2022

Background: Lignocellulosic biomass has many functionalities that hold huge potential for material, energy or chemistry applications. To support advanced applications, the biomass must be milled into ultrafine powder to increase reactivity. This milling unit operation needs to be fully mastered to deliver high-quality standard end-products. Here we studied the relationship between the characteristics of the starting lignocellulosic plant material and the properties of the resulting ultrafine powder in different ball-mill process routes.

Methods: Two lignocellulosic biomasses (pine bark and wheat straw) with contrasted compositional and mechanical properties were milled using three ball-mill set-ups delivering different balances of impact force and attrition force. The resulting powders were analysed for particle characteristics (size, agglomeration extent, shape) and powder flow properties (compressibility, cohesion) using a dynamic powder rheometer.

Results: Pine bark is more amenable to a fast particle size reduction than the fibrous wheat straw. The resulting pine bark powders appear less compressible but much more cohesive than the straw powders due to particle shape, density and composition factors. The mill set-up working by attrition as dominant mechanical force (vibratory ball mill) produced a mix of large, elongated particles and higher amounts of fines as it acts mainly by erosion, the resulting powder being more prone to agglomerate due to the abundance of fines. The mill set-up working by impact as dominant mechanical force (rotary ball mill) produced more evenly distributed particle sizes and shapes. The resulting powder is less prone to agglomerate due to a preferential fragmentation mechanism.

Conclusions: The attrition-dominant mill yields powders with dispersed particle sizes and shapes and the poorest flow properties, while the impact-dominant mill yields more agglomeration-prone powders. The mill set-up working with impact and attrition as concomitant mechanical forces (stirred ball mill) produces powders with better reactivity and flow properties compared to rotary and vibratory mills.
Rationale and design of the brain magnetic resonance imaging protocol for FutureMS: a longitudinal multi-centre study of newly diagnosed patients with relapsing-remitting multiple sclerosis in Scotland
Authors: Meijboom Rozanna , Wiseman Stewart J. , York Elizabeth N. , Bastin Mark E. , Valdés Hernández Maria del C. , Thrippleton Michael J. , Mollison Daisy , White Nicole , Kampaite Agniete , Ng Kee Kwong Koy , Rodriguez Gonzalez David , Job Dominic , Weaver Christine , Kearns Patrick K. A. , Connick Peter , Chandran Siddharthan , Waldman Adam D.
Published: March 2022

Introduction: Multiple sclerosis (MS) is a chronic neuroinflammatory and neurodegenerative disease. MS prevalence varies geographically and is notably high in Scotland. Disease trajectory varies significantly between individuals and the causes for this are largely unclear. Biomarkers predictive of disease course are urgently needed to allow improved stratification for current disease modifying therapies and future targeted treatments aimed at neuroprotection and remyelination. Magnetic resonance imaging (MRI) can detect disease activity and underlying damage non-invasively in vivo at the micro and macrostructural level. FutureMS is a prospective Scottish longitudinal multi-centre cohort study, which focuses on deeply phenotyping patients with recently diagnosed relapsing-remitting MS (RRMS). Neuroimaging is a central component of the study and provides two main primary endpoints for disease activity and neurodegeneration. This paper provides an overview of MRI data acquisition, management and processing in FutureMS. FutureMS is registered with the Integrated Research Application System (IRAS, UK) under reference number 169955.

Methods and analysis: MRI is performed at baseline (N=431) and 1-year follow-up, in Dundee, Glasgow and Edinburgh (3T Siemens) and in Aberdeen (3T Philips), and managed and processed in Edinburgh. The core structural MRI protocol comprises T1-weighted, T2-weighted, FLAIR and proton density images. Primary imaging outcome measures are new/enlarging white matter lesions (WML) and reduction in brain volume over one year. Secondary imaging outcome measures comprise WML volume as an additional quantitative structural MRI measure, rim lesions on susceptibility-weighted imaging, and microstructural MRI measures, including diffusion tensor imaging and neurite orientation dispersion and density imaging metrics, relaxometry, magnetisation transfer (MT) ratio, MT saturation and derived g-ratio measures.

Conclusions: FutureMS aims to reduce uncertainty around disease course and allow for targeted treatment in RRMS by exploring the role of conventional and advanced MRI measures as biomarkers of disease severity and progression in a large population of RRMS patients in Scotland.
Evaluation of revitalisation projects in Poland using the Maslin Multi-Dimensional Matrix. Heading towards green & social revitalisation
Authors: Starczewski Tomasz , Krzysztof Rogatka , Kowalski Mateusz
Published: March 2022

One of the greatest challenges currently facing cities is the evaluation of the revitalisation process, i.e., verifying whether and to what extent it has been successful. This assessment is important as it will determine the extent to which the revitalisation needs of a place have been met. The aim of this article is to present the results of the evaluation of a post-revitalisation space made by its users and to determine the usefulness of the Maslin Multi-Dimensional Matrix (MMDM) method used. This is the first attempt, not previously reported in the literature, to use the MMDM for evaluating revitalisation. According to research, projects of an integration and environmental character and those improving security were the most appreciated and at the same time had the best revitalising effect on the Bydgoskie Przedmieście district in Toruń, Poland. The lowest ratings were given to infrastructural projects or those dedicated to narrow social groups (alternative arts). The MMDM method should be considered an appropriate tool for evaluating revitalisation.
Finite State Mean Field Games with Wright–Fisher Common Noise as Limits ofN-Player Weighted Games
Authors: Bayraktar Erhan , Cecchin Alekos , Cohen Asaf , Delarue François
Published: March 2022

Forcing finite state mean field games by a relevant form of common noise is a subtle issue, which has been addressed only recently. Among others, one possible way is to subject the simplex valued dynamics of an equilibrium by a so-called Wright–Fisher noise, very much in the spirit of stochastic models in population genetics. A key feature is that such a random forcing preserves the structure of the simplex, which is nothing but, in this setting, the probability space over the state space of the game. The purpose of this article is, hence, to elucidate the finite-player version and, accordingly, prove that N-player equilibria indeed converge toward the solution of such a kind of Wright–Fisher mean field game. Whereas part of the analysis is made easier by the fact that the corresponding master equation has already been proved to be uniquely solvable under the presence of the common noise, it becomes however more subtle than in the standard setting because the mean field interaction between the players now occurs through a weighted empirical measure. In other words, each player carries its own weight, which, hence, may differ from [Formula: see text] and which, most of all, evolves with the common noise.
Asthma: Disadvantaged children at greater risk of the condition persisting into adulthood
Authors: Lepkowska Dorothy
Published: March 2022

New research shows that children with asthma living in a social disadvantaged environment are at an increased risk of the condition persisting into adulthood, as well as having more asthma attacks and hospitalisations.
My experience of an alternative placement
Authors: Campbell Katie
Published: March 2022

Katie Campbell shares her experience of a last minute alternative to her placement as part of her SCPHN School Nursing student journey, after her initial alternative placement broke down, and what she learned.
Label-free monitoring of spatiotemporal changes in the stem cell cytoskeletons in time-lapse phase-contrast microscopy
Authors: Jiang Ching-Fen , Sun Yu-Man
Published: March 2022

Investigation of the dynamic structural changes in the actin cytoskeleton during cell migration provides crucial information about the physiological conditions of a stem cell during in-vitro culture. Here we proposed a quantitative analytical model associated with texture extraction with cell tracking techniques for in situ monitoring of the cytoskeletal density change of stem cells in phase-contrast microscopy without fluorescence staining. The reliability of the model in quantifying the texture density with different orientation was first validated using a series of simulated textural images. The capability of the method to reflect the spatiotemporal regulation of the cytoskeletal structure of a living stem cell was further proved by applying it to a set of 72 h phase-contrast microscopic video of the growth dynamics of mesenchymal stem cells in vitro culture.
Overcoming acoustic crosstalk in the BOTDA sensor with a bidirectional frequency-modulated probe
Authors: Liu Can , Yan Lianshan , Li Zonglei , Zhou Yin , He Haijun , Pan Wei , Luo Bin
Published: March 2022

Conventional Brillouin optical time-domain analyzer (BOTDA) with a frequency-modulated probe (FMP) could avoid non-local effects, while still suffering from the acoustic crosstalk between different frequencies. The induced Brillouin frequency shift (BFS) measurement errors over the whole sensing fiber link reduce system certainty subsequently. A BOTDA scheme with a bidirectional frequency-modulated probe (BFMP) is proposed to overcome such an effect. It utilizes BFMP to generate the crosstalk of the same magnitude and opposite direction to compensate each other. Experimental results indicate that the pulse interval of the coded sequence could be reduced to ∼500 ns to improve the measurement efficiency and BFS estimation errors (∼2.2 MHz) over 117.46-km sensor link are eliminated simultaneously.
Multi-layer programmable spectral anti-counterfeiting based on quantum dots inkjet printing
Authors: Cui Hao , Li Junwei , Wei Kai , Zhang Guosheng , Zhou And Sheng
Published: March 2022

High security and convenient operation have been the aim of the anticounterfeiting field. An anticounterfeit system in which multiple information are written on an overlapping area with quantum dot (QD) inks of different fluorescence wavelengths that combines spectroscopy technology for information identification is proposed in this study. Because the emission spectra of QDs can be tuned by simply changing the size, ultraviolet (UV) glue mixed with different sizes of CdSe/ZnS QDs is used as the printing ink with different fluorescence wavelengths. Software-design labels with different information are printed on the overlapping area using inks with different luminescent QDs. The printed information can only be identified by the bandpass filter with the corresponding wavelength under UV light. Under natural light, the information cannot be identified by the naked eye. In the proposed anticounterfeiting system, the excitation light and filter are both indispensables. Our method makes the fabrication of anticounterfeit labels flexible in design, fast in production, and high in information concealment. Meanwhile, the proposed system is quick and convenient, which has huge application potential in the field of display and anticounterfeiting.
Laboratory system for optical coherence tomography (OCT) using a laser plasma source of soft x-rays and extreme ultraviolet and focusing ellipsoidal optics
Authors: Arikkatt Antony Jose , Węgrzyński Łukasz , Bartnik Andrzej , Fiedorowicz Henryk , Wachulak Przemysław
Published: March 2022

Optical coherence tomography (OCT) with the use of soft x-rays (SXR) and extreme ultraviolet (EUV) has been recently demonstrated [Fuchs et al. Sci. Rep. 6, 20658 (2016)10.1038/srep20658; Fuchs et al. Optica 4, 903 (2017)10.1364/OPTICA.4.000903]. This new imaging technique, named XCT, makes it possible to obtain cross-sectional and tomographic images of objects with nanometer spatial resolution. The article presents a newly developed laboratory system for XCT using a compact laser plasma light source operating in the SXR and EUV spectral ranges. The source is based on a gas puff target containing Kr gas or a Kr/Xe gas mixture irradiated with nanosecond laser pulses from an Nd:YAG laser. The use of the gas puff target enables efficient emission of SXR and EUV radiation without generating target debris associated with laser ablation when using a solid target. The system is equipped with an ellipsoidal mirror to collect radiation from the source and focus on the imaged object. The XCT measurements are made by processing the spectrum of the radiation reflected from the object recorded with a transmission grating spectrometer equipped with an identical focusing mirror and a CCD camera. The paper presents the characterization and optimization of the new XCT system and its application to the measurements of layered nanostructures.
RosettaSurf—A surface-centric computational design approach
Authors: Scheck Andreas , Rosset Stéphane , Defferrard Michaël , Loukas Andreas , Bonet Jaume , Vandergheynst Pierre , Correia Bruno E.
Published: March 2022

Proteins are typically represented by discrete atomic coordinates providing an accessible framework to describe different conformations. However, in some fields proteins are more accurately represented as near-continuous surfaces, as these are imprinted with geometric (shape) and chemical (electrostatics) features of the underlying protein structure. Protein surfaces are dependent on their chemical composition and, ultimately determine protein function, acting as the interface that engages in interactions with other molecules. In the past, such representations were utilized to compare protein structures on global and local scales and have shed light on functional properties of proteins. Here we describe RosettaSurf, a surface-centric computational design protocol, that focuses on the molecular surface shape and electrostatic properties as means for protein engineering, offering a unique approach for the design of proteins and their functions. The RosettaSurf protocol combines the explicit optimization of molecular surface features with a global scoring function during the sequence design process, diverging from the typical design approaches that rely solely on an energy scoring function. With this computational approach, we attempt to address a fundamental problem in protein design related to the design of functional sites in proteins, even when structurally similar templates are absent in the characterized structural repertoire. Surface-centric design exploits the premise that molecular surfaces are, to a certain extent, independent of the underlying sequence and backbone configuration, meaning that different sequences in different proteins may present similar surfaces. We benchmarked RosettaSurf on various sequence recovery datasets and showcased its design capabilities by generating epitope mimics that were biochemically validated. Overall, our results indicate that the explicit optimization of surface features may lead to new routes for the design of functional proteins.
SavvyCNV: Genome-wide CNV calling from off-target reads
Authors: Laver Thomas W. , De Franco Elisa , Johnson Matthew B. , Patel Kashyap A. , Ellard Sian , Weedon Michael N. , Flanagan Sarah E. , Wakeling Matthew N.
Published: March 2022

Identifying copy number variants (CNVs) can provide diagnoses to patients and provide important biological insights into human health and disease. Current exome and targeted sequencing approaches cannot detect clinically and biologically-relevant CNVs outside their target area. We present SavvyCNV, a tool which uses off-target read data from exome and targeted sequencing data to call germline CNVs genome-wide. Up to 70% of sequencing reads from exome and targeted sequencing fall outside the targeted regions. We have developed a new tool, SavvyCNV, to exploit this ‘free data’ to call CNVs across the genome. We benchmarked SavvyCNV against five state-of-the-art CNV callers using truth sets generated from genome sequencing data and Multiplex Ligation-dependent Probe Amplification assays. SavvyCNV called CNVs with high precision and recall, outperforming the five other tools at calling CNVs genome-wide, using off-target or on-target reads from targeted panel and exome sequencing. We then applied SavvyCNV to clinical samples sequenced using a targeted panel and were able to call previously undetected clinically-relevant CNVs, highlighting the utility of this tool within the diagnostic setting. SavvyCNV outperforms existing tools for calling CNVs from off-target reads. It can call CNVs genome-wide from targeted panel and exome data, increasing the utility and diagnostic yield of these tests. SavvyCNV is freely available at https://github.com/rdemolgen/SavvySuite.
Simulation atomic force microscopy for atomic reconstruction of biomolecular structures from resolution-limited experimental images
Authors: Amyot Romain , Marchesi Arin , Franz Clemens M. , Casuso Ignacio , Flechsig Holger
Published: March 2022

Atomic force microscopy (AFM) can visualize the dynamics of single biomolecules under near-physiological conditions. However, the scanning tip probes only the molecular surface with limited resolution, missing details required to fully deduce functional mechanisms from imaging alone. To overcome such drawbacks, we developed a computational framework to reconstruct 3D atomistic structures from AFM surface scans, employing simulation AFM and automatized fitting to experimental images. We provide applications to AFM images ranging from single molecular machines, protein filaments, to large-scale assemblies of 2D protein lattices, and demonstrate how the obtained full atomistic information advances the molecular understanding beyond the original topographic AFM image. We show that simulation AFM further allows for quantitative molecular feature assignment within measured AFM topographies. Implementation of the developed methods into the versatile interactive interface of the BioAFMviewer software, freely available at www.bioafmviewer.com, presents the opportunity for the broad Bio-AFM community to employ the enormous amount of existing structural and modeling data to facilitate the interpretation of resolution-limited AFM images.
Identifying effective interventions to promote consumption of protein-rich foods from lower ecological footprint sources: A systematic literature review
Authors: Ronto Rimante , Saberi Golsa , Leila Robbers Gianna Maxi , Godrich Stephanie , Lawrence Mark , Somerset Shawn , Fanzo Jessica , Chau Josephine Y.
Published: March 2022

Addressing overconsumption of protein-rich foods from high ecological footprint sources can have positive impacts on health such as reduction of non-communicable disease risk and protecting the natural environment. With the increased attention towards development of ecologically sustainable diets, this systematic review aimed to critically review literature on effectiveness of those interventions aiming to promote protein-rich foods from lower ecological footprint sources. Five electronic databases (Medline, Web of Science, Scopus, Embase and Global Health) were searched for articles published up to January 2021. Quantitative studies were eligible for inclusion if they reported on actual or intended consumption of protein-rich animal-derived and/or plant-based foods; purchase, or selection of meat/plant-based diet in real or virtual environments. We assessed 140 full-text articles for eligibility of which 51 were included in this review. The results were narratively synthesised. Included studies were categorised into individual level behaviour change interventions (n = 33) which included education, counselling and self-monitoring, and micro-environmental/structural behaviour change interventions (n = 18) which included menu manipulation, choice architecture and multicomponent approaches. Half of individual level interventions (52%) aimed to reduce red/processed meat intake among people with current/past chronic conditions which reduced meat intake in the short term. The majority of micro-environmental studies focused on increasing plant-based diet in dining facilities, leading to positive dietary changes. These findings point to a clear gap in the current evidence base for interventions that promote plant-based diet in the general population.
Cerebral paragonimiasis: Clinicoradiological features and serodiagnosis using recombinant yolk ferritin
Authors: Kim Jeong-Geun , Ahn Chun-Seob , Kang Insug , Shin Jong-Wook , Jeong Hae-Bong , Nawa Yukifumi , Kong Yoon
Published: March 2022

Cerebral paragonimiasis (CP), caused by aberrant migration of Paragonimus worms, frequently invokes serious illness. The causal relationship between the lesion characteristics and patients’ symptoms has poorly been understood. CP serodiagnosis has not been properly evaluated to date. A total of 111 CP cases were diagnosed in our laboratory between 1982 and 2003. This study retrospectively assessed the clinical and imaging characteristics of the 105 patients along with the evaluation of diagnostic potentials of recombinant P. westermani yolk ferritin (rPwYF) by enzyme-linked immunosorbent assay (ELISA) employing patients’ sera and cerebrospinal fluids (CSFs). We analyzed 60 male and 45 female patients; 50 early-stage patients with non-calcified enhancing nodule(s) (median age, 38 years; interquartile range [IQR], 24.75–52; median symptom duration, 0.75 years; IQR, 0.2–2) and 54 chronic cases having calcified lesion(s) (median age, 33 years; IQR, 25–41; median symptom duration, 10 years; IQR, 5–20). One patient showed a normal neuroimage. The patients were largely diagnosed in their 30s. The parietal lobe was most commonly affected, followed by occipital, frontal, and temporal lobes. Twenty-six patients had lesions encompassing ≥ two lobes. The patients complained mainly of seizures, headaches, hemiparesis, and focal neurologic deficits (P < 0.001). Seizures and visual defects were predominant in patients with calcified lesion(s) (P < 0.001). The diagnostic sensitivity and specificity of rPwYF against serum/CSF were 100%/97% and 97.2%/92.5%, respectively. The specific IgG antibody levels against rPwYF in sera and CSFs showed a positive correlation (r = 0.59). The clinical manifestations of the early-stage patients might be associated with cortical lesions or meningeal irritation, while those in the chronic stage were caused by conglomerated space-occupying lesions. rPwYF would be useful for the serodiagnosis of both early and chronic CP cases.
Pose-invariant matching for non-rigid 3D models using Isomap
Authors: Jin Hairong , Huang Haichao , Wang Zhiqiang , Xie Yuqing , Zhou Xinyue , Huang Liming , Hong Zhouzhenyan
Published: March 2022

The wide usage of 3D mesh models greatly increases the importance of an effective matching algorithm for them. In this paper, we propose a novel 3D model matching algorithm. Firstly, vertices on the input 3D mesh models are mapped to 1D space by employing Isomap. A pose-invariant feature set is then constructed from the vertices in 1D space. Finally, the similarity between any two 3D models can be computed by comparing their feature sets. Experimental results show that the algorithm is not only invariant to translation, rotation, scaling, but also invariant to different poses of 3D models. Additionally, the algorithm is robust to noise.