CURTAIN – A unique web-based tool for exploration and sharing of MS-based proteomics data

To facilitate analysis and sharing of mass spectrometry (MS)-based proteomics data, we created online tools called CURTAIN (https://curtain.proteo.info) and CURTAIN-PTM (https://curtainptm.proteo.info) with an accompanying series of video tutorials (https://www.youtube.com/@CURTAIN-me6hl). These are designed to enable non-MS experts to interactively peruse volcano plots and deconvolute primary experimental data so that replicates can be visualized in bar charts or violin plots and exported in publication-ready format. They also allow assessment of overall experimental quality by correlation matrix and profile plot analysis. After making a selection of protein "hits", the user can analyze known domain structure, AlphaFold predicted structure, reported interactors, relative expression as well as disease links. CURTAIN-PTM permits analysis of all identified PTM sites on protein(s) of interest with selected databases. CURTAIN-PTM also links with the Kinase Library to predict upstream kinases that may phosphorylate sites of interest. We provide examples of the utility of CURTAIN and CURTAIN-PTM in analyzing how targeted degradation of the PPM1H Rab phosphatase that counteracts the Parkinson's LRRK2 kinase impacts cellular protein levels and phosphorylation sites. We also reanalyzed a ubiquitylation dataset, characterizing the PINK1-Parkin pathway activation in primary neurons, revealing data of interest not highlighted previously. CURTAIN and CURTAIN-PTM are free to use and open source, enabling researchers to share and maximize the impact of their proteomics data. We advocate that MS data published in volcano plot format be reported containing a shareable CURTAIN weblink, thereby allowing readers to better analyze and exploit the data.</p

Factors associated with antenatal care adequacy in rural and urban contexts-results from two health and demographic surveillance sites in Vietnam

<p>Abstract</p> <p>Background</p> <p>Antenatal Care (ANC) is universally considered important for women and children. This study aims to identify factors, demographic, social and economic, possibly associated with three ANC indicators: number of visits, timing of visits and content of services. The aim is also to compare the patterns of association of such factors between one rural and one urban context in northern Vietnam.</p> <p>Methods</p> <p>Totally 2,132 pregnant women were followed from identification of pregnancy until birth in two Health and Demographic Surveillance Sites (HDSS). Information was obtained through quarterly face to face interviews.</p> <p>Results</p> <p>Living in the rural area was significantly associated with lower adequate use of ANC compared to living in the urban area, both regarding quantity (number and timing of visits) and content. Low education, living in poor households and exclusively using private sector ANC in both sites and self employment, becoming pregnant before 25 years of age and living in poor communities in the rural area turned out to increase the risk for overall inadequate ANC. High risk pregnancy could not be demonstrated to be associated with ANC adequacy in either site. The medical content of services offered was often inadequate, in relation to the national recommendations, especially in the private sector.</p> <p>Conclusion</p> <p>Low education, low economic status, exclusive use of private ANC and living in rural areas were main factors associated with risk for overall inadequate ANC use as related to the national recommendations. Therefore, interventions focussing on poor and less educated women, especially in rural areas should be prioritized. They should focus the importance of early attendance of ANC and sufficient use of core services. Financial support for poor and near poor women should be considered. Providers of ANC should be educated and otherwise influenced to provide sufficient core services. Adherence to ANC content guidelines must be improved through enhanced supervision, particularly in the private sector.</p

Is this pill an antibiotic or a painkiller? Improving the identification of oral antibiotics for better use

In this Viewpoint, we discuss how the identification of oral antibiotics and their distinction from other commonly used medicines can be challenging for consumers, suppliers, and health-care professionals. There is a large variation in the names that people use to refer to antibiotics and these often relate to their physical appearance, although antibiotics come in many different physical presentations. We also reflect on how the physical appearance of medicine influences health care and public health by affecting communication between patients and health-care professionals, dispensing , medicine use, and the public understanding of health campaigns. Furthermore, we report expert and stakeholder consultations on improving the identification of oral antibiotics and discuss next steps towards a new identification system for antibiotics. We propose to use the physical appearance as a tool to support and nudge awareness about antibiotics and their responsible use

Efficacy against pneumococcal carriage and the immunogenicity of reduced-dose (0 + 1 and 1 + 1) PCV10 and PCV13 schedules in Ho Chi Minh City, Viet Nam: a parallel, single-blind, randomised controlled trial

Background Interest in reduced-dose pneumococcal conjugate vaccine (PCV) schedules is growing, but data on their ability to provide direct and indirect protection are scarce. We evaluated 1 + 1 (at 2 months and 12 months) and 0 + 1 (at 12 months) schedules of PCV10 or PCV13 in a predominately unvaccinated population. Methods In this parallel, single-blind, randomised controlled trial, healthy infants aged 2 months were recruited from birth records in three districts in Ho Chi Minh City, Vietnam, and assigned (4:4:4:4:9) to one of five groups: PCV10 at 12 months of age (0 + 1 PCV10), PCV13 at 12 months of age (0 + 1 PCV13), PCV10 at 2 months and 12 months of age (1 + 1 PCV10), PCV13 at 2 months and 12 months of age (1 + 1 PCV13), and unvaccinated control. Outcome assessors were masked to group allocation, and the infants' caregivers and those administering vaccines were not. Nasopharyngeal swabs collected at 6 months, 12 months, 18 months, and 24 months were analysed for pneumococcal carriage. Blood samples collected from a subset of participants (200 per group) at various timepoints were analysed by ELISA and opsonophagocytic assay. The primary outcome was the efficacy of each schedule against vaccine-type carriage at 24 months, analysed by intention to treat for all those with a nasopharyngeal swab available. This trial is registered at ClinicalTrials.gov, NCT03098628. Findings 2501 infants were enrolled between March 8, 2017, and July 24, 2018 and randomly assigned to study groups (400 to 0 + 1 PCV10, 400 to 0 + 1 PCV13, 402 to 1 + 1 PCV10, 401 to 1 + 1 PCV13, and 898 to control). Analysis of the primary endpoint included 341 participants for 0 + 1 PCV10, 356 0 + 1 PCV13, 358 1 + 1 PCV10, 350 1 + 1 PCV13, and 758 control. At 24 months, a 1 + 1 PCV10 schedule reduced PCV10-type carriage by 58% (95% CI 25 to 77), a 1 + 1 PCV13 schedule reduced PCV13-type carriage by 65% (42 to 79), a 0 + 1 PCV10 schedule reduced PCV10-type carriage by 53% (17 to 73), and a 0 + 1 PCV13 schedule non-significantly reduced PCV13-type carriage by 25% (–7 to 48) compared with the unvaccinated control group. Reactogenicity and serious adverse events were similar across groups. Interpretation A 1 + 1 PCV schedule greatly reduces vaccine-type carriage and is likely to generate substantial herd protection and provide some degree of individual protection during the first year of life. Such a schedule is suitable for mature PCV programmes or for introduction in conjunction with a comprehensive catch-up campaign, and potentially could be most effective given as a mixed regimen (PCV10 then PCV13). A 0 + 1 PCV schedule has some effect on carriage along with a reasonable immune response and could be considered for use in humanitarian crises or remote settings. Funding Bill & Melinda Gates Foundation. Translation For the Vietnamese translation of the abstract see Supplementary Materials section

The baseline characteristics and interim analyses of the high-risk sentinel cohort of the Vietnam Initiative on Zoonotic InfectiONS (VIZIONS)

The Vietnam Initiative for Zoonotic Infections (VIZIONS) includes community-based 'high-risk sentinel cohort' (HRSC) studies investigating individuals at risk of zoonotic infection due to occupational or residential exposure to animals. A total of 852 HRSC members were recruited between March 2013 and August 2014 from three provinces (Ha Noi, Dak Lak, and Dong Thap). The most numerous group (72.8%) corresponded to individuals living on farms, followed by slaughterers (16.3%) and animal health workers (8.5%). Nasal/pharyngeal and rectal swabs were collected from HRSC members at recruitment and after notifying illness. Exposure to exotic animals (including wild pigs, porcupine, monkey, civet, bamboo rat and bat) was highest for the Dak Lak cohort (53.7%), followed by Ha Noi (13.7%) and Dong Thap (4.0%). A total of 26.8% of individuals reported consumption of raw blood over the previous year; 33.6% slaughterers reported no use of protective equipment at work. Over 686 person-years of observation, 213 episodes of suspect infectious disease were notified, equivalent of 0.35 reports per person-year. Responsive samples were collected from animals in the farm cohort. There was noticeable time and space clustering of disease episodes suggesting that the VIZIONS set up is also suitable for the formal epidemiological investigation of disease outbreaks

Магнитные характеристики твердых растворов Ni1–xMxMnSb (M = Ti, V, Cr)

The results of an experiment on the study of the crystal and magnetic structures of substitutional solid solutions of the Ni0.90M0.10MnSb (M = Ti, V, Cr) systems using thermal neutron diffraction in the temperature range ~ 3–300 K are presented. It is found that all the studied compositions have ferromagnetic ordering along the c axis. In the spectra of Ni0.90V0.10MnSb and Ni0.90Cr0.10MnSb solid solutions, a reflection appears in the region 2Θ = 28.6°, which indicates the formation of antiferromagnetic ordering. It has been found that this reflection disappears at a temperature T = 75 K in Ni0.90V0.10MnSb, while it is observed in the spectrum of Ni0.90Cr0.10MnSb over the entire temperature range under study. Within the framework of density functional theory (DFT), an ab initio calculation of the crystal structure and magnetic moments for Ni1–xMxMnSb (M = Ti, V, Cr; x = 0; 0.125; 0.250) was carried out. It has been established that titanium, vanadium, and chromium ions participate in electron transfer only with Mn and Sb ions. The DFT results predict the existence of magnetic moments for Ti, V, and Cr ions. It was found that the spins of Ti, V, and Cr ions are antiferromagnetically coupled with the spins of Mn and Ni ions. The results obtained are of interest for the development of new concepts and models of structural design, which makes it possible to synthesize fundamentally new functional materials with already specified physical properties.Представлены результаты эксперимента по изучению кристаллической и магнитной структур твердых растворов замещения систем Ni0,90M0,10MnSb (M = Ti, V, Cr) с помощью дифракции тепловых нейтронов в интервале температур ~ 3–300 К. Обнаружено, что все исследуемые составы обладают ферромагнитным упорядочением вдоль оси с. На спектрах твердых растворов Ni0,90V0,10MnSb и Ni0,90Сr0,10MnSb в области 2Θ = 28,6° отмечено появление рефлекса, который указывает на формирование антиферромагнитного упорядочения. Установлено, что данный рефлекс исчезает при температуре T = 75 К в Ni0,90V0,10MnSb, а на спектре Ni0,90Cr0,10MnSb он наблюдается во всем исследуемом диапазоне температур. В рамках теории функционала плотности (DFT) проведен ab initio расчет кристаллической структуры и магнитных моментов для Ni1–xMxMnSb (M = Ti, V, Cr; x = 0; 0,125; 0,250). Установлено, что ионы титана, ванадия и хрома участвуют в переносе электрона только с ионами Mn и Sb. Результаты DFT предсказывают существование магнитных моментов у ионов Ti, V и Cr. Обнаружено, что спины ионов Ti, V и Cr антиферромагнитно связаны со спинами ионов Mn и Ni. Полученные результаты представляют интерес для разработки новых концепции и моделей структурного дизайна, при котором возможен синтез принципиально новых функциональных материалов с уже заданными физическими свойствами