Taxonomy of endosymbiotic bacteria from a novel Lupinus sp. (Lupinus mariae-josephi) endemic of a limed-alkaline soil habitat in Southeastern Spain

Lupinus mariae-josephi is a recently described Lupinus species (Pascual 2004) endemic of a Southeastern area of Spain with soils singularly of high pH and active lime content where it is endangered due to the reduced size of its habitat. Ten isolates of L. mariae-josephi endosymbiotic bacteria were obtained using trap-plants and soils from five sampling points within a native plant population area in Llombai (Valencia, Spain). The microsymbionts are extra-slow (ultrabradytrophic) growing bacteria with phenotypic and symbiotic characteristics singularly different from Bradyrhizobium strains nodulating other Lupinus spp. thriving in the Iberian Peninsula and adapted to growth in acidic soils. Cross-inoculation experiments revealed that these L. mariae-josephi endosymbiotic bacteria isolates are unable to nodulate or efficiently fix nitrogen with other Lupinus spp. Their phylogenetic status was examined by a multilocus sequence analysis of four housekeeping genes (16S rDNA, glnII, recA, atpD) and the symbiotic nodC gene. The 16S rDNA phylogenetic analysis showed that L. mariae-josephi isolates are related to strains nodulating Retama spp. in northeastern Algeria (Boulila et al., 2009), Phaseolus lunatus from Peru (Ormeño-Orrillo et al., 2006), as well as to B. elkanii, B. jicamae and B. pachyrhizi species, forming a new clade (Clade I) within the Bradyrhizobium genus. All the single and concatenated glnII+recA and glnII+recA+atpD analyses consistently support the existence of Clade I, and also revealed that, within this clade, the L. mariae-josephi endosymbiotic bacteria belong to a single evolutionary lineage that also includes strains nodulating Retama spp. from northeastern Algeria. Within this new Bradyrhizobium lineage, the phylogenetic analyses performed showed essentially convergent results indicating that the tested L. mariae-josephi isolates nested in three sub-groups that might correspond to novel sister Bradyrhizobium species. Bradyrhizobium Clade I is highly differentiated from the Bradyrhizobium clade (Clade II) that includes currently named Bradyrhizobium species and well-delineated unnamed genospecies. Singularly, all the endosymbiotic bacteria from Lupinus species adapted to acid soils in the Iberian Peninsula and tested in this study are included in Clade II. They are related either to strains of the B. canariense or B. japonicum lineages. The phylogenetic analysis based on the symbiotic nodC gene showed that L. mariae-josephi endosymbiotic bacteria define a novel branch in the nodC Bradyrhizobium tree. This branch groups together with a branch that gathers isolates from recently studied legume symbiosis such as isolates from Retama spp., which suggests the existence of a common unique ancestor for the symbiotic genes of these two groups of bradyrhizobia. In contrast, the symbiotic genes of isolates from other Lupinus spp. from the Iberian Peninsula are clearly related to the B. canariense lineage. The allopatric (geographic) speciation of the L. mariae-josephi bradyrhizobia may result from the colonization of a singular habitat, such as the basic and high calcium carbonate soils of the Valencia area, by its unique legume host

Building sustainable capacity for health research in africa through cloud computing applications

Access to information and continuous education represent critical factors for physicians and researchers over the world. For African professionals, this situation is even more problematic due to the frequently difficult access to technological infrastructures and basic information. Both education and information technologies (e.g., including hardware, software or networking) are expensive and unaffordable for many African professionals. Thus, the use of e-learning and an open approach to information exchange and software use have been already proposed to improve medical informatics issues in Africa. In this context, the AFRICA BUILD project, supported by the European Commission, aims to develop a virtual platform to provide access to a wide range of biomedical informatics and learning resources to professionals and researchers in Africa. A consortium of four African and four European partners work together in this initiative. In this framework, we have developed a prototype of a cloud-computing infrastructure to demonstrate, as a proof of concept, the feasibility of this approach. We have conducted the experiment in two different locations in Africa: Burundi and Egypt. As shown in this paper, technologies such as cloud computing and the use of open source medical software for a large range of case present significant challenges and opportunities for developing countries, such as many in Africa

Phenotypic and phylogenetic characterization of endosymbiotic bacteria from Lupinus mariae-josephi

Lupinus mariae-josephi is a Lupinus species that thrives in a Southeastern area of Spain (Valencia) in soils of singularly high pH and active lime content. It is nodulated by extra-slow growing bacteria symbiotically and phylogenetically distant to endosymbiotic strains nodulating other Lupinus sp. native of the Iberian Peninsula and adapted to growth in acid soils. Cross-inoculation experiments revealed that the L. mariae-josephi endosymbiotic bacteria are unable to nodulate or efficiently fix nitrogen with well-known Lupinus spp. Their species affiliation was examined by a multilocus sequence analysis of four housekeeping genes (16S rDNA, glnII, recA, atpD) and the symbiotic nodC gene. Single and concatenated phylogenetic analyses of these genes consistently revealed that L. mariae-josephi endosymbiotic bacteria belong to a clade, within the Bradyrhizobium genus, highly differentiated from the Bradyrhizobium clade that includes currently named Bradyrhizobium species as well as the endosymbiotic bacteria from Lupinus species tested in this study. Within this new clade the L. mariae-josephi bacteria nested in several subgroup that may correspond to novel sister species. The phylogenetic analysis based on the nodC gene showed that L. mariae-josephi endosymbiotic bacteria define a novel branch of the nodC Bradyrhizobium tree and likely have a common unique ancestor for the symbiotic genes with nodule isolates from Retama spp

Accessing and managing open medical resources in Africa over the Internet

Recent commentaries have proposed the advantages of using open exchange of data and informatics resources for improving health-related policies and patient care in Africa. Yet, in many African regions, both private medical and public health information systems are still unaffordable. Open exchange over the social Web 2.0 could encourage more altruistic support of medical initiatives. We have carried out some experiments to demonstrate the feasibility of using this approach to disseminate open data and informatics resources in Africa. After the experiments we developed the AFRICA BUILD Portal, the first Social Network for African biomedical researchers. Through the AFRICA BUILD Portal users can access in a transparent way to several resources. Currently, over 600 researchers are using distributed and open resources through this platform committed to low connections

Commissioning Plan of the IFMIF-DONES Accelerator

IFMIF-DONES (International Fusion Materials Irradiation Facility- DEMO-Oriented Neutron Early Source) - a powerful neutron irradiation facility for studies and certification of materials to be used in fusion reactors - is planned as part of the European roadmap to fusion electricity. Its main goal will be to characterize and to qualify materials under irradiation in a neutron field similar to the one faced in a fusion reactor. The intense neutron source is produced by impinging deuterons, from high-power linear deuteron accelerator, on a liquid lithium curtain. The facility has accomplished the preliminary design phase and is currently in its detailed design phase. At the present stage, it is important to have a clear understanding of how the commissioning of the facility will be performed, especially the commissioning of a 5 MW CW deuteron beam, together with the lithium curtain and the beam optimization for the neutron irradiation. In this contribution, the present plans for the hardware and beam commissioning of the accelerator will be given, focusing on the most critical aspects of the tiered approach and on the integration of the procedure with the lithium and tests systems

Defining the genotypic and phenotypic spectrum of X-linked MSL3-related disorder

Purpose We sought to delineate the genotypic and phenotypic spectrum of female and male individuals with X-linked, MSL3-related disorder (Basilicata-Akhtar syndrome). Methods Twenty-five individuals (15 males, 10 females) with causative variants in MSL3 were ascertained through exome or genome sequencing at ten different sequencing centers. Results We identified multiple variant types in MSL3 (ten nonsense, six frameshift, four splice site, three missense, one in-frame-deletion, one multi-exon deletion), most proven to be de novo, and clustering in the terminal eight exons suggesting that truncating variants in the first five exons might be compensated by an alternative MSL3 transcript. Three-dimensional modeling of missense and splice variants indicated that these have a deleterious effect. The main clinical findings comprised developmental delay and intellectual disability ranging from mild to severe. Autism spectrum disorder, muscle tone abnormalities, and macrocephaly were common as well as hearing impairment and gastrointestinal problems. Hypoplasia of the cerebellar vermis emerged as a consistent magnetic resonance image (MRI) finding. Females and males were equally affected. Using facial analysis technology, a recognizable facial gestalt was determined. Conclusion Our aggregated data illustrate the genotypic and phenotypic spectrum of X-linked, MSL3-related disorder (Basilicata-Akhtar syndrome). Our cohort improves the understanding of disease related morbidity and allows us to propose detailed surveillance guidelines for affected individuals

Defining the genotypic and phenotypic spectrum of X-linked MSL3-related disorder

PURPOSE: We sought to delineate the genotypic and phenotypic spectrum of female and male individuals with X-linked, MSL3-related disorder (Basilicata-Akhtar syndrome). METHODS: Twenty-five individuals (15 males, 10 females) with causative variants in MSL3 were ascertained through exome or genome sequencing at ten different sequencing centers. RESULTS: We identified multiple variant types in MSL3 (ten nonsense, six frameshift, four splice site, three missense, one in-frame-deletion, one multi-exon deletion), most proven to be de novo, and clustering in the terminal eight exons suggesting that truncating variants in the first five exons might be compensated by an alternative MSL3 transcript. Three-dimensional modeling of missense and splice variants indicated that these have a deleterious effect. The main clinical findings comprised developmental delay and intellectual disability ranging from mild to severe. Autism spectrum disorder, muscle tone abnormalities, and macrocephaly were common as well as hearing impairment and gastrointestinal problems. Hypoplasia of the cerebellar vermis emerged as a consistent magnetic resonance image (MRI) finding. Females and males were equally affected. Using facial analysis technology, a recognizable facial gestalt was determined. CONCLUSION: Our aggregated data illustrate the genotypic and phenotypic spectrum of X-linked, MSL3-related disorder (Basilicata-Akhtar syndrome). Our cohort improves the understanding of disease related morbidity and allows us to propose detailed surveillance guidelines for affected individuals

Impact of COVID-19 on cardiovascular testing in the United States versus the rest of the world

Objectives: This study sought to quantify and compare the decline in volumes of cardiovascular procedures between the United States and non-US institutions during the early phase of the coronavirus disease-2019 (COVID-19) pandemic. Background: The COVID-19 pandemic has disrupted the care of many non-COVID-19 illnesses. Reductions in diagnostic cardiovascular testing around the world have led to concerns over the implications of reduced testing for cardiovascular disease (CVD) morbidity and mortality. Methods: Data were submitted to the INCAPS-COVID (International Atomic Energy Agency Non-Invasive Cardiology Protocols Study of COVID-19), a multinational registry comprising 909 institutions in 108 countries (including 155 facilities in 40 U.S. states), assessing the impact of the COVID-19 pandemic on volumes of diagnostic cardiovascular procedures. Data were obtained for April 2020 and compared with volumes of baseline procedures from March 2019. We compared laboratory characteristics, practices, and procedure volumes between U.S. and non-U.S. facilities and between U.S. geographic regions and identified factors associated with volume reduction in the United States. Results: Reductions in the volumes of procedures in the United States were similar to those in non-U.S. facilities (68% vs. 63%, respectively; p = 0.237), although U.S. facilities reported greater reductions in invasive coronary angiography (69% vs. 53%, respectively; p < 0.001). Significantly more U.S. facilities reported increased use of telehealth and patient screening measures than non-U.S. facilities, such as temperature checks, symptom screenings, and COVID-19 testing. Reductions in volumes of procedures differed between U.S. regions, with larger declines observed in the Northeast (76%) and Midwest (74%) than in the South (62%) and West (44%). Prevalence of COVID-19, staff redeployments, outpatient centers, and urban centers were associated with greater reductions in volume in U.S. facilities in a multivariable analysis. Conclusions: We observed marked reductions in U.S. cardiovascular testing in the early phase of the pandemic and significant variability between U.S. regions. The association between reductions of volumes and COVID-19 prevalence in the United States highlighted the need for proactive efforts to maintain access to cardiovascular testing in areas most affected by outbreaks of COVID-19 infection

Mortality and pulmonary complications in patients undergoing surgery with perioperative SARS-CoV-2 infection: an international cohort study

Background: The impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on postoperative recovery needs to be understood to inform clinical decision making during and after the COVID-19 pandemic. This study reports 30-day mortality and pulmonary complication rates in patients with perioperative SARS-CoV-2 infection. Methods: This international, multicentre, cohort study at 235 hospitals in 24 countries included all patients undergoing surgery who had SARS-CoV-2 infection confirmed within 7 days before or 30 days after surgery. The primary outcome measure was 30-day postoperative mortality and was assessed in all enrolled patients. The main secondary outcome measure was pulmonary complications, defined as pneumonia, acute respiratory distress syndrome, or unexpected postoperative ventilation. Findings: This analysis includes 1128 patients who had surgery between Jan 1 and March 31, 2020, of whom 835 (74·0%) had emergency surgery and 280 (24·8%) had elective surgery. SARS-CoV-2 infection was confirmed preoperatively in 294 (26·1%) patients. 30-day mortality was 23·8% (268 of 1128). Pulmonary complications occurred in 577 (51·2%) of 1128 patients; 30-day mortality in these patients was 38·0% (219 of 577), accounting for 81·7% (219 of 268) of all deaths. In adjusted analyses, 30-day mortality was associated with male sex (odds ratio 1·75 [95% CI 1·28–2·40], p\textless0·0001), age 70 years or older versus younger than 70 years (2·30 [1·65–3·22], p\textless0·0001), American Society of Anesthesiologists grades 3–5 versus grades 1–2 (2·35 [1·57–3·53], p\textless0·0001), malignant versus benign or obstetric diagnosis (1·55 [1·01–2·39], p=0·046), emergency versus elective surgery (1·67 [1·06–2·63], p=0·026), and major versus minor surgery (1·52 [1·01–2·31], p=0·047). Interpretation: Postoperative pulmonary complications occur in half of patients with perioperative SARS-CoV-2 infection and are associated with high mortality. Thresholds for surgery during the COVID-19 pandemic should be higher than during normal practice, particularly in men aged 70 years and older. Consideration should be given for postponing non-urgent procedures and promoting non-operative treatment to delay or avoid the need for surgery. Funding: National Institute for Health Research (NIHR), Association of Coloproctology of Great Britain and Ireland, Bowel and Cancer Research, Bowel Disease Research Foundation, Association of Upper Gastrointestinal Surgeons, British Association of Surgical Oncology, British Gynaecological Cancer Society, European Society of Coloproctology, NIHR Academy, Sarcoma UK, Vascular Society for Great Britain and Ireland, and Yorkshire Cancer Research

Why Are Outcomes Different for Registry Patients Enrolled Prospectively and Retrospectively? Insights from the Global Anticoagulant Registry in the FIELD-Atrial Fibrillation (GARFIELD-AF).

Background: Retrospective and prospective observational studies are designed to reflect real-world evidence on clinical practice, but can yield conflicting results. The GARFIELD-AF Registry includes both methods of enrolment and allows analysis of differences in patient characteristics and outcomes that may result. Methods and Results: Patients with atrial fibrillation (AF) and ≥1 risk factor for stroke at diagnosis of AF were recruited either retrospectively (n = 5069) or prospectively (n = 5501) from 19 countries and then followed prospectively. The retrospectively enrolled cohort comprised patients with established AF (for a least 6, and up to 24 months before enrolment), who were identified retrospectively (and baseline and partial follow-up data were collected from the emedical records) and then followed prospectively between 0-18 months (such that the total time of follow-up was 24 months; data collection Dec-2009 and Oct-2010). In the prospectively enrolled cohort, patients with newly diagnosed AF (≤6 weeks after diagnosis) were recruited between Mar-2010 and Oct-2011 and were followed for 24 months after enrolment. Differences between the cohorts were observed in clinical characteristics, including type of AF, stroke prevention strategies, and event rates. More patients in the retrospectively identified cohort received vitamin K antagonists (62.1% vs. 53.2%) and fewer received non-vitamin K oral anticoagulants (1.8% vs . 4.2%). All-cause mortality rates per 100 person-years during the prospective follow-up (starting the first study visit up to 1 year) were significantly lower in the retrospective than prospectively identified cohort (3.04 [95% CI 2.51 to 3.67] vs . 4.05 [95% CI 3.53 to 4.63]; p = 0.016). Conclusions: Interpretations of data from registries that aim to evaluate the characteristics and outcomes of patients with AF must take account of differences in registry design and the impact of recall bias and survivorship bias that is incurred with retrospective enrolment. Clinical Trial Registration: - URL: http://www.clinicaltrials.gov . Unique identifier for GARFIELD-AF (NCT01090362)