Algorithms to automatically quantify the geometric similarity of anatomical surfaces

We describe new approaches for distances between pairs of 2-dimensional surfaces (embedded in 3-dimensional space) that use local structures and global information contained in inter-structure geometric relationships. We present algorithms to automatically determine these distances as well as geometric correspondences. This is motivated by the aspiration of students of natural science to understand the continuity of form that unites the diversity of life. At present, scientists using physical traits to study evolutionary relationships among living and extinct animals analyze data extracted from carefully defined anatomical correspondence points (landmarks). Identifying and recording these landmarks is time consuming and can be done accurately only by trained morphologists. This renders these studies inaccessible to non-morphologists, and causes phenomics to lag behind genomics in elucidating evolutionary patterns. Unlike other algorithms presented for morphological correspondences our approach does not require any preliminary marking of special features or landmarks by the user. It also differs from other seminal work in computational geometry in that our algorithms are polynomial in nature and thus faster, making pairwise comparisons feasible for significantly larger numbers of digitized surfaces. We illustrate our approach using three datasets representing teeth and different bones of primates and humans, and show that it leads to highly accurate results.Comment: Changes with respect to v1, v2: an Erratum was added, correcting the references for one of the three datasets. Note that the datasets and code for this paper can be obtained from the Data Conservancy (see Download column on v1, v2

GenBank

GenBank® is a comprehensive database that contains publicly available nucleotide sequences for more than 300 000 organisms named at the genus level or lower, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole genome shotgun (WGS) and environmental sampling projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the European Molecular Biology Laboratory Nucleotide Sequence Database in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bi-monthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI homepage: www.ncbi.nlm.nih.gov

Variety of Clostridium difficile PCR ribotypes in pigs arriving at the slaughterhouse

Food products of animal origin might play a role in interspecies transmission of C. difficile. In pigs, Clostridium difficile can cause neonatal enteritis and can be isolated from faeces from both diseased and healthy animals. To determine the prevalence of C. difficile in Dutch pigs arriving at the slaughterhouse a pilot study was conducted at one slaughterhouse in the Netherlands. Rectal faecal samples were taken from fifty slaughtering pigs from ten farms just after the pigs were sedated. These samples were examined using a real time PCR (BD GeneOhmTM Cdiff Assay), in combination with culturing after enrichment. Using real time PCR, none of the faecal samples were found to be positive for C. difficile while after culturing 14 samples (coming from pigs from nine different farms) were found to be positive for C. difficile. The positive samples derived from 9 different farms and encompassed seven different ribotypes

GenBank

GenBank® is a comprehensive database that contains publicly available nucleotide sequences for more than 250 000 formally described species. These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole-genome shotgun (WGS) and environmental sampling projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI home page: www.ncbi.nlm.nih.gov

Препятствия, стоящие перед эффективной национальной программой лечения туберкулеза: пример Индии = Obstacles facing an effective national tuberculosis treatment program: a case study of India

Туберкулез (ТБ) - это заболевание, имеющее большое значение и входящее в десятку основных причин смертности в мире. Индия несет непропорционально большое бремя, на которую приходится более четверти случаев в мире. За последние 25 лет Индийское правительство расширило национальную программу диагностики и лечения, охватывающую всю страну. Тем не менее, накопились данные о том, что общая заболеваемость туберкулезом и случаи множественной лекарственной устойчивости не изменились и даже могут увеличиваться. В этой статье мы обсудим возможные препятствия, стоящие перед индийской программой по борьбе с ТБ. К ним относятся в основном нерегулируемый частный сектор, недостаточное финансирование Индийского бюджета здравоохранения, недостаточные местные знания о болезни у поставщиков противотуберкулезных препаратов, пробелы в текущем каскаде медицинской помощи (от диагностики до лечения), преобладающая социальная стигматизация туберкулеза и высокая распространенность других важных сопутствующих заболеваний, таких как нищета, диабет, ВИЧ и курение. Для достижения всеобщего, высококачественного охвата диагностикой и лечением ключевое значение имеет эффективное сотрудничество с частным сектором. Кроме того, эффективные, основанные на фактических данных инновационные мобильные технологии, а также использование медицинских работников местных сообществ могут принести пользу наиболее социально маргинализированным слоям населения, на которых эти препятствия оказывают наибольшее влияние в Индийском обществе. / Tuberculosis (TB) is a disease of major significance, being one of the top ten causes of death globally. India bears a disproportionately large burden, accounting for more than a quarter of the world’s cases. Over the last 25 years, the Indian Government has scaled-up a national diagnostics and treatment program to cover the entire country. However, there is accumulating evidence that the total TB incidence and that of multi-drug resistance cases has not changed and may even be increasing. In this article, we discuss possible obstacles facing the Indian TB control programme. These include a largely unregulated private sector, underfunding of the Indian health budget, inadequate local knowledge about the disease in TB medication providers, gaps in the current cascade of care (from diagnosis to treatment), prevailing social stigma for TB and a high prevalence of other important comorbidities, such as poverty, diabetes, HIV and smoking. To achieve universal, high quality diagnostics and treatment coverage, effective collaboration with the private sector is key. Furthermore, efficient, evidence-based innovative mobile technologies plus the use of local community healthcare workers can benefit the most socially-marginalized upon whom these obstacles most impact in Indian society

Variation in C - reactive protein response according to host and mycobacterial characteristics in active tuberculosis

BACKGROUND: The C - reactive protein (CRP) response is often measured in patients with active tuberculosis (TB) yet little is known about its relationship to clinical features in TB, or whether responses differ between ethnic groups or with different Mycobacterium tuberculosis (M.tb) strain types. We report the relationship between baseline serum CRP prior to treatment and disease characteristics in a metropolitan population with TB resident in a low TB incidence region. METHODS: People treated for TB at four London, UK sites between 2003 and 2014 were assessed and data collected on the following characteristics: baseline CRP level; demographics (ethnicity, gender and age); HIV status; site of TB disease; sputum smear (in pulmonary cases) and culture results. The effect of TB strain-type was also assessed in culture-positive pulmonary cases using VNTR typing data. RESULTS: Three thousands two hundred twenty-two patients were included in the analysis of which 72 % had a baseline CRP at or within 4 weeks prior to starting TB treatment. CRP results were significantly higher in culture positive cases compared to culture negative cases: median 49 mg/L (16-103 mg/L) vs 19 mg/L (IQR 5-72 mg/L), p = <0.001. In those with pulmonary disease, smear positive cases had a higher CRP than smear negative cases: 67 mg/L (31-122 mg/L) vs 24 mg/L (7-72 mg/L), p < 0.001. HIV positive cases had higher baseline CRPs than HIV negative cases: 75 mg/L (26-136 mg/L) vs 37 mg/L (10-88 mg/L), p <0.001. Differing sites of disease were associated with differences in baseline CRP: locations that might be expected to have a high mycobacterial load (e.g. pulmonary disease and disseminated disease) had a significantly higher CRP than those such as skin, lymph node or CNS disease, where the mycobacterial load is typically low in HIV negative subjects. In a multivariable log-scale linear regression model adjusting for host characteristics and M.tb strain type, infection with the East African Indian strain was associated with significantly lower baseline-CRP (fold-change in CRP 0.51 (0.34-0.77), p < 0.01). CONCLUSIONS: Host and mycobacterial factors are strongly associated with baseline CRP response in tuberculosis. This analysis suggests that there are important differences in innate immune response according to ethnicity, Mtb strain type and site of disease. This may reflect differing mycobacterial loads or host immune responses

Improved treatment completion for tuberculosis patients: The case for a dedicated social care team

OBJECTIVES: The increasing social needs of people with Tuberculosis (TB), and the poor adherence to anti-TB therapy (ATT) associated with homelessness, drug or alcohol abuse, and prison history, led us to introduce a social care team (SCT) to support patient engagement with care within this low TB incidence setting. METHODS: Using a risk assessment, patients with social risk factors (SRF) for non-adherence to ATT are identified and a referral made to the SCT, who then provide intensive casework support for areas including homelessness, housing, benefits, debt and immigration. Retrospective data analysis of the social care database from 2017 to 2019 was conducted. Patients who were (n = 170) and were not referred to the SCT (n = 734) were compared. RESULTS: Patients referred were significantly more likely to complete treatment for TB than those not (88.2% versus 77.7% respectively, p = 0.0025), irrespective of receipt of Directly/Video Observed Therapy and adjusting for confounders. CONCLUSIONS: This paper demonstrates important evidence for the positive impact of a dedicated SCT within a TB service, and these improved treatment outcomes provide a strong argument for development of similar SCTs within UK TB services and similar healthcare settings

Observational study to estimate the changes in the effectiveness of bacillus Calmette-Guérin (BCG) vaccination with time since vaccination for preventing tuberculosis in the UK.

Until recently, evidence that protection from the bacillus Calmette-Guérin (BCG) vaccination lasted beyond 10 years was limited. In the past few years, studies in Brazil and the USA (in Native Americans) have suggested that protection from BCG vaccination against tuberculosis (TB) in childhood can last for several decades. The UK's universal school-age BCG vaccination programme was stopped in 2005 and the programme of selective vaccination of high-risk (usually ethnic minority) infants was enhanced. To assess the duration of protection of infant and school-age BCG vaccination against TB in the UK. Two case-control studies of the duration of protection of BCG vaccination were conducted, the first on minority ethnic groups who were eligible for infant BCG vaccination 0-19 years earlier and the second on white subjects eligible for school-age BCG vaccination 10-29 years earlier. TB cases were selected from notifications to the UK national Enhanced Tuberculosis Surveillance system from 2003 to 2012. Population-based control subjects, frequency matched for age, were recruited. BCG vaccination status was established from BCG records, scar reading and BCG history. Information on potential confounders was collected using computer-assisted interviews. Vaccine effectiveness was estimated as a function of time since vaccination, using a case-cohort analysis based on Cox regression. In the infant BCG study, vaccination status was determined using vaccination records as recall was poor and concordance between records and scar reading was limited. A protective effect was seen up to 10 years following infant vaccination [&lt; 5 years since vaccination: vaccine effectiveness (VE) 66%, 95% confidence interval (CI) 17% to 86%; 5-10 years since vaccination: VE 75%, 95% CI 43% to 89%], but there was weak evidence of an effect 10-15 years after vaccination (VE 36%, 95% CI negative to 77%; p = 0.396). The analyses of the protective effect of infant BCG vaccination were adjusted for confounders, including birth cohort and ethnicity. For school-aged BCG vaccination, VE was 51% (95% CI 21% to 69%) 10-15 years after vaccination and 57% (95% CI 33% to 72%) 15-20 years after vaccination, beyond which time protection appeared to wane. Ascertainment of vaccination status was based on self-reported history and scar reading. The difficulty in examining vaccination sites in older women in the high-risk minority ethnic study population and the sparsity of vaccine record data in the later time periods precluded robust assessment of protection from infant BCG vaccination &gt; 10 years after vaccination. Infant BCG vaccination in a population at high risk for TB was shown to provide protection for at least 10 years, whereas in the white population school-age vaccination was shown to provide protection for at least 20 years. This evidence may inform TB vaccination programmes (e.g. the timing of administration of improved TB vaccines, if they become available) and cost-effectiveness studies. Methods to deal with missing record data in the infant study could be explored, including the use of scar reading. The National Institute for Health Research Health Technology Assessment programme. During the conduct of the study, Jonathan Sterne, Ibrahim Abubakar and Laura C Rodrigues received other funding from NIHR; Ibrahim Abubakar and Laura C Rodrigues have also received funding from the Medical Research Council. Punam Mangtani received funding from the Biotechnology and Biological Sciences Research Council

Applications of patching to quadratic forms and central simple algebras

This paper provides applications of patching to quadratic forms and central simple algebras over function fields of curves over henselian valued fields. In particular, we use a patching approach to reprove and generalize a recent result of Parimala and Suresh on the u-invariant of p-adic function fields, for p odd. The strategy relies on a local-global principle for homogeneous spaces for rational algebraic groups, combined with local computations.Comment: 48 pages; connectivity now required in the definition of rational group; beginning of Section 4 reorganized; other minor change