Annual Report 2014 - Institute of Ion Beam Physics and Materials Research

This past year 2014 was the year when we finally completely arrived as a “full member” in the Helmholtz Association. This is related to the successfully passed research evaluation in the framework of the Program Oriented Funding (POF), which will give us a stable and predictable funding for the next five years (2015 – 2019). This is particularly true for our large-scale user facilities, like the Ion Beam Center (IBC) and the electron accelerator ELBE with the free-electron laser. Most of our activities are assigned to the program “From Matter to Materials and Life” within the research area “Matter”, in cooperation with several other German Helmholtz Centers. Our in-house research is performed in three so-called research themes, as depicted in the schematic below. What is missing there for simplicity is a small part of our activities in the program “Nuclear Waste Management and Safety” within the research area “Energy”. Our research and facilities were well appreciated by the evaluation committee, who made the following judgement about the Ion Beam Center: “The Ion Beam Centre (IBC) of HZDR is an internationally leading ion-beam facility (with ion energies ranging from several eV to several tens of MeV). At both the national and international level it is one of the key players and is unique in its kind. The synergy between forefront research and user service has been leading to a very good publication output for both in-house research and user research. … The very broad range of beam energies, the versatility of techniques and applications – both for ion beam modification of materials and for ion-beam analysis – makes the IBC unique in its kind. … The strength of IBC is that its activities are based on a combination of forefront research and user service, which mutually interact in synergy and strengthen one another. In turn, this synergy has been leading to a very good publication output for both in-house research and user research.” In order to make our Annual Report a bit more compact, we have decided to include only four full journal papers this year. This was also triggered by the fact that our publication activities have turned out be become more diverse, in more diverse journals than in the past, and often through longer papers, which would be too long to reprint them here. However, apart from the constantly quantitatively high publication output, we succeeded to publish in excellent journals such as Nature Physics, Nano Letters and Physical Review Letters, in fields as diverse as ion beam physics, magnetism and terahertz spectroscopy. Two of our scientists, Dr. Artur Erbe and Dr. Alexej Pashkin obtained their Habilitation in 2014, both at University of Konstanz. For the first time, we are hosting an Emmy Noether Young Investigator Group funded by the Deutsche Forschungsgemeinschaft (DFG); the group works on the hot topic of magnonics and is headed by Dr. Helmut Schultheiß. Finally we would like to cordially thank all partners, friends, and organizations who supported our progress in 2014. Special thanks are due to the Executive Board of the Helmholtz-Zentrum Dresden-Rossendorf, the Minister of Science and Arts of the Free State of Saxony, and the Minister of Education and Research of the Federal Government of Germany. Numerous partners from universities, industry and research institutes all around the world contributed essentially, and play a crucial role for the further development of the institute. Last but not least, the directors would like to thank again all IIM staff for their efforts and excellent contributions in 2014

Use of Procalcitonin and C-Reactive Protein to Evaluate Vaccine Efficacy against Pneumonia

BACKGROUND: Pneumonia remains the leading cause of death in young children. The poor specificity of chest radiographs (CXRs) to diagnose pneumococcal pneumonia may underestimate the efficacy of pneumococcal conjugate vaccine in preventing pneumococcal pneumonia. METHODS AND FINDINGS: The efficacy of nine-valent pneumococcal conjugate vaccine among children not infected with HIV (21%; 95% confidence interval, 1%–37%) increased when CXR-confirmed pneumonia was associated with serum C-reactive protein of 120 mg/l (12mg/dl) or more and procalcitonin of 5.0 ng/ml or more (64%; 95% confidence interval, 23%–83%). Similar results were observed in children infected with HIV. CONCLUSION: C-reactive protein and procalcitonin improve the specificity of CXR to diagnose pneumococcal pneumonia and may be useful for the future evaluation of the effectiveness of pneumococcal conjugate vaccine in preventing pneumococcal pneumonia

A comparison of the magnetic properties of Proton- and Iron-implanted graphite

In this work we have investigated the changes of the magnetic properties of highly oriented pyrolytic graphite samples after irradiation either with $\sim 3 \times 10^{14}$ protons or $3.5 \times 10^{13} ... 3.5 \times 10^{14}$ iron ions with energies in the MeV range. Our results show that iron and proton irradiations can produce similar paramagnetic contributions depending on the implantation temperature. However, only protons induce a ferromagnetic effect.Comment: 4 pages with three figures. To be published in EPJ

Crop protection from animals based on machine learning

This paper will discuss the present level of research and development on human-wildlife conflicts, there are bad interactions between humans and wild animals that are bad for both the resources of the human population as well as the ecosystems of wildlife. Animal detection has an impact on both human food security and animal welfare because it arises from the conflict between humans and wildlife over natural resources. As the population has grown and many communities' land use patterns have changed, these disputes have become more prevalent in recent years. The Mobile Net SSD type is used in this automatic intrusion and deterrent system for enhanced performance. When a dangerous animal is discovered, the system emits an alarm sound and notifies the relevant authorities, alerting them to the discovery. It is more human- friendly due to the quick detection process, and it is more animal-friendly due to the gentle repulsive process

Twisted large cellular fibroma of the ovary with pelvic effusion-revisiting incomplete demons Meigs’ syndrome

Fibromas of the ovary are benign tumours arising from the stromal component of the ovary. They represent 1% of ovarian neoplasms and are generally benign. The cellular subtype accounts for around 10% of these and is a tumour of uncertain malignant potential. Recurrence may occur or it could be associated with peritoneal implants. Usually these are solid tumours, sometimes with small areas of cystic degeneration. Occasionally, large fibromas may undergo torsion causing acute abdominal pain and generally tends to occur in post-menopausal women. The solid areas, ORADS and ascites simulated a malignant ovarian tumour on both MRI, USG and gross pathologic examination. Here we present a case of a postmenopausal woman presented with abdominal pain and postprandial vomiting with a large twisted ovarian fibroma leading to diagnostic and therapeutic challenges masquerading as a malignant ovarian neoplasm

Molecular-genetic characterization of human parvovirus B19 prevalent in Kerala State, India

peer-reviewedBackground Human parvovirus B19V is a DNA virus, and a member of the family Parvoviridae, that causes various clinical manifestations, from asymptomatic to persistent infection that is associated with different autoimmune diseases. The parvovirus B19 evolves with a very high mutation rate that is closer to those of existing RNA viruses. Globally circulating B19V is currently classified into three genotypes, but their distribution is not spatially and temporally correlated. Except for a few recent reports on B19V entry into the human host and its genetic diversity, there is a lack of sufficient studies on this virus from distinct geographical locations and no clear understanding of its evolution has been documented. Methods To better understand the evolution of the Human parvo B19V virus from India's southern part, a geographically distinct location with no reports of B19V genomes, we have screened for B19V in 456 suspected cases using VP1/2 surface marker genes, and its characteristics were studied in detail. Amongst 456 clinically suspected B19V samples, 7.2% (33/456) were found positive by nested PCR (nPCR) were subsequently validated by real-time PCR, Sanger sequencing, and metagenome analysis. Results Human parvovirus B19 infection was shown among 33 of 456 patients when tested by nPCR; 30 among these were also positive by qPCR and were subsequently confirmed by sequencing 75% nPCR positive samples and 76% qPCR positive samples were from patients with age. ≥ 50 years respectively (Additional file 1: Table S1). The complete VP1/2 gene assembly from the South Indian strain showed three novel mutations (T122A, V128I, I283V), which might significantly impact the stability and virulence of the B19V virus circulating in this part of the world. These mutations might be crucial for its adaptive evolutionary strategies facilitating the spread and infectivity potential of the virus. In maximum likelihood phylogeny of VP1/2 sequences, the South Indian B19V strain forms a separate clade closer to the existing genotype two strains circulating worldwide. Conclusion Our study contributes to a better understanding of the human parvovirus's genetic and evolutionary characteristics in South India. Also, it highlights the possibility that a positive selection pressure acting on VP1/2 could increase the survival and replication capabilities of the viruses

Comparative determination of HIV-1 co-receptor tropism by Enhanced Sensitivity Trofile, gp120 V3-loop RNA and DNA genotyping

BACKGROUND: Trofile is the prospectively validated HIV-1 tropism assay. Its use is limited by high costs, long turn-around time, and inability to test patients with very low or undetectable viremia. We aimed at assessing the efficiency of population genotypic assays based on gp120 V3-loop sequencing for the determination of tropism in plasma viral RNA and in whole-blood viral DNA. Contemporary and follow-up plasma and whole-blood samples from patients undergoing tropism testing via the enhanced sensitivity Trofile (ESTA) were collected. Clinical and clonal geno2pheno[coreceptor] (G2P) models at 10% and at optimised 5.7% false positive rate cutoff were evaluated using viral DNA and RNA samples, compared against each other and ESTA, using Cohen's kappa, phylogenetic analysis, and area under the receiver operating characteristic (AUROC). RESULTS: Both clinical and clonal G2P (with different false positive rates) showed good performances in predicting the ESTA outcome (for V3 RNA-based clinical G2P at 10% false positive rate AUROC = 0.83, sensitivity = 90%, specificity = 75%). The rate of agreement between DNA- and RNA-based clinical G2P was fair (kappa = 0.74, p < 0.0001), and DNA-based clinical G2P accurately predicted the plasma ESTA (AUROC = 0.86). Significant differences in the viral populations were detected when comparing inter/intra patient diversity of viral DNA with RNA sequences. CONCLUSIONS: Plasma HIV RNA or whole-blood HIV DNA V3-loop sequencing interpreted with clinical G2P is cheap and can be a good surrogate for ESTA. Although there may be differences among viral RNA and DNA populations in the same host, DNA-based G2P may be used as an indication of viral tropism in patients with undetectable plasma viremia

Diverse values of nature for sustainability

Twenty-five years since foundational publications on valuing ecosystem services for human well-being(1,2), addressing the global biodiversity crisis(3) still implies confronting barriers to incorporating nature's diverse values into decision-making. These barriers include powerful interests supported by current norms and legal rules such as property rights, which determine whose values and which values of nature are acted on. A better understanding of how and why nature is (under)valued is more urgent than ever(4). Notwithstanding agreements to incorporate nature's values into actions, including the Kunming-Montreal Global Biodiversity Framework (GBF)(5) and the UN Sustainable Development Goals(6), predominant environmental and development policies still prioritize a subset of values, particularly those linked to markets, and ignore other ways people relate to and benefit from nature(7). Arguably, a 'values crisis' underpins the intertwined crises of biodiversity loss and climate change(8), pandemic emergence(9) and socio-environmental injustices(10). On the basis of more than 50,000 scientific publications, policy documents and Indigenous and local knowledge sources, the Intergovernmental Platform on Biodiversity and Ecosystem Services (IPBES) assessed knowledge on nature's diverse values and valuation methods to gain insights into their role in policymaking and fuller integration into decisions(7,11). Applying this evidence, combinations of values-centred approaches are proposed to improve valuation and address barriers to uptake, ultimately leveraging transformative changes towards more just (that is, fair treatment of people and nature, including inter- and intragenerational equity) and sustainable futures