Infrastructures for agroecological field research – Current situation and future prospectsPosition paper of the DFG Senate Commission on Agroecosystem Research

Groß angelegte und langfristig etablierte Feldversuche sind ein zentrales Element der standortbezogenen Agrarwissenschaften. Die Erarbeitung des Grundlagenwissens zu standortangepassten bzw. regionalspezifischen Produktivitätspotentialen von Pflanzenbeständen sowie die Entwicklung von ökologisch vertretbaren, innovativen Produktionssystemen mit hoher Produktivität und Resi­lienz erfordern leistungsfähige Forschungsinfrastrukturen, die relevante Gradienten an Klima- und Bodenfaktoren abdecken und den interdisziplinären Dialog fördern. Das Positionspapier der Senatskommission für Agrar­öko­systemforschung der Deutschen Forschungsgemeinschaft stellt den Status quo und die zukünftigen Anforderungen an Feldversuchseinrichtungen dar. Zur Optimierung des agrarwissenschaftlichen Feldversuchswesens wird angeregt, in einem Netzwerk aus Versuchseinrichtungen Landschaftsfunktionen prototypisch abzubilden, um in einem interdisziplinären Ansatz Flächenproduktivität, Resilienz und Ressourceneffizienz landschaftsspezifisch untersuchen zu können. Des Weiteren ist es erforderlich, der wissenschaftlichen Community standardisierte Daten in Datenrepositorien zur Verfügung zu stellen. DOI: 10.5073/JfK.2014.07.02, https://doi.org/10.5073/JfK.2014.07.02Large-scale, long-term field experiments are a core element of site-specific agricultural science. To create basic knowledge of site-adapted and regional agricultural production potentials as well as to develop ecologically sound and innovative plant production systems with high productivity and resilience requires high-capacity research infrastructures that cover relevant climatic gradients and soils and that promote an interdisciplinary dialog. The position paper of the Senate Commission on Agroecosystem Research of the Deutsche Forschungsgemeinschaft shows the current status and future requirements on infrastructures for agroecological field research. To optimize the infrastructure for agricultural field trials, a network of experimental sites that cover prototype landscape functions is suggested, enabling interdisciplinary investigations of productivity, resilience and resource efficiency in the landscape context. Further it is necessary to provide standardized data in open access data repositories to the scientific community. DOI: 10.5073/JfK.2014.07.02, https://doi.org/10.5073/JfK.2014.07.0

Nonpromoter methylation of the CDKN2A gene with active transcription is associated with improved locoregional control in laryngeal squamous cell carcinoma

We previously reported a novel association between CDKN2A nonpromoter methylation and transcription (ARF/INK4a) in human papillomavirus associated oropharyngeal tumors. In this study we assessed whether nonpromoter CDKN2A methylation in laryngeal squamous cell carcinomas (LXSCC) conferred a similar association with transcription that predicted patient outcome. We compared DNA methylation and ARF/INK4a RNA expression levels for the CDKN2A locus using the Illumina HumanMethylation27 beadchip and RT-PCR in 43 LXSCC tumor samples collected from a prospective study of head and neck cancer patients treated at Montefiore Medical Center (MMC). Validation was performed using RNAseq data on 111 LXSCC tumor samples from the Cancer Genome Atlas (TCGA). The clinical relevance of combined nonpromoter CDKN2A methylation and transcription was assessed by multivariate Cox regression for locoregional recurrence on a subset of 69 LXSCC patients with complete clinicopathologic data from the MMC and TCGA cohorts. We found evidence of CDKN2A nonpromoter hypermethylation in a third of LXSCC from our MMC cohort, which was significantly associated with increased ARF and INK4a RNA expression (Wilcoxon rank-sum, P = 0.007 and 0.003, respectively). A similar association was confirmed in TCGA samples (Wilcoxon rank-sum test P < 0.0001 for ARF and INK4a). Patients with CDKN2A hypermethylation or high ARF/INK4a expression were significantly less likely to develop a locoregional recurrence compared to those with neither of the features, independent of other clinicopatholgic risk factors (adjusted hazard ratio=0.21, 95% confidence interval:0.05-0.81). These results support the conclusion that CDKN2A nonpromoter methylation is associated with increased ARF and INK4a RNA expression, and improved locoregional control in LXSCC

An analysis of the effect of statins on the risk of Non-Hodgkin\u27s Lymphoma in the Women\u27s Health Initiative cohort.

Statins have been shown to induce a phosphoprotein signature that modifies MYC (myelocytomatosis viral oncogene) activation and to have anti-inflammatory activity that may impact the risk of Non-Hodgkin\u27s lymphoma (NHL). We analyzed the relationship between statins and risk of NHL using data from the Women\u27s Health Initiative (WHI). The study population included 161,563 postmenopausal women ages 50-79 years from which 712 cases of NHL were diagnosed after 10.8 years of follow-up. Information on statin use and other risk factors was collected by self- and interviewer-administered questionnaires. Multivariable-adjusted HR and 95% CI evaluating the relationship between statin use at baseline, as well as in a time-dependent manner and risk of NHL, were computed from Cox proportional hazards analyses. A separate analysis was performed for individual NHL subtypes: diffuse large B-Cell lymphoma (DLBCL) (n = 228), follicular lymphoma (n = 169), and small lymphocytic lymphoma (n = 74). All statistical tests were two-sided. There was no significant association between use of statins at baseline and risk of NHL (HR 0.85, 95% C.I. 0.67-1.08). However, in the multivariable-adjusted time-dependent models, statin use was associated with a borderline lower risk of NHL (HR 0.81, 95% C.I. 0.66-1.00). Considering subtypes of NHL, statin use was associated with a lower risk of DLBCL (HR 0.62, 95% C.I. 0.42-0.91). This effect was driven by lipophilic statins (HR 0.62, 95% C.I. 0.40-0.96). In the WHI, statins were associated with a lower overall risk of DLBCL, particularly attributable to lipophilic statins. These results may have impact on primary or secondary prevention of NHL, particularly DLBCL

Acquisition and Persistence of Human Papillomavirus 16 (HPV-16) and HPV-18 Among Men With High-HPV Viral Load Infections in a Circumcision Trial in Kisumu, Kenya

Background. Circumcision and lower human papillomavirus (HPV) viral loads in men are possibly associated with a reduced risk of HPV transmission to women. However, the association between male circumcision and HPV viral load remains unclear

Cervical, Anal and Oral HPV in an Adolescent Inner-City Health Clinic Providing Free Vaccinations

Published human papillomavirus (HPV) vaccine trials indicate efficacy is strongest for those naive to the vaccine-types. However, few high-risk young women have been followed and cervical HPV has been the predominant outcome measure.We collected cervical and anal swabs, as well as oral rinse specimens from 645 sexually active inner-city young females attending a large adolescent health-clinic in New York City that offers free care and HPV vaccination. Specimens were tested for HPV-DNA using a MY09/MY11-PCR system. Type-specific prevalence of HPV at each anatomic site was compared for individuals by vaccination dose using generalized estimating equation logistic regression models.The majority of subjects reported being of non-Caucasian (92%) and/or Hispanic ethnicity (61%). Median age was 18 years (range:14-20). All had practiced vaginal sex, a third (33%) practiced anal sex, and most (77%) had also engaged in oral sex. At enrollment, 21% had not received the vaccine and 51% had received three doses. Prevalent HPV infection at enrollment was detected in 54% of cervical, 42% of anal and 20% of oral specimens, with vaccine types present in 7%, 6% and 1% of specimens, respectively. Comparing prevalence for vaccine types, the detection of HPV in the cervix of vaccinated compared to unvaccinated adolescents was significantly reduced: HPV6/11 (odds ratio [OR] = 0.19, 95%CI:0.06-0.75), HPV16 (OR = 0.31, 95%CI:0.11-0.88) and HPV18 (OR = 0.14, 95%CI:0.03-0.75). For anal HPV, the risk of detecting vaccine types HPV6/11 (OR = 0.27, 95%CI:0.10-0.72) and HPV18(OR = 0.12, 95%CI:0.01-1.16) were significantly reduced for vaccinated adolescents however, the risk for HPV16 was not significantly decreased (OR = 0.63, 95%CI:0.18-2.20).HPV Prevalence is extremely high in inner-city female adolescents. Administration of the HPV vaccine reduced the risk for cervical HPV; however continued follow-up is required to assess the protection for HPV at all sites in young women with high exposure

Sustainable and resource efficient intensivation of crop production – Perspectives of agro-ecosystem researchPolicy paper of the DFG Senate Commission on Agroecosystem Research

Mit dem vorliegenden Grundsatzpapier zeigt die Senatskommission für Agrarökosystemforschung Perspektiven für die Grundlagenforschung zur nachhaltigen Erhöhung der Kulturpflanzenproduktion auf.Agrarsysteme stehen im Spannungsfeld zwischen steigendem Bedarf an landwirtschaftlichen Produkten, der Verknappung der Ressourcen, dem Verlust der Biodiversität und dem Klimawandel. Die für das Jahr 2050 prognostizierte notwendige Ertragssteigerung zur Sicherstellung des Bedarfs an Nahrungsmitteln kann, ohne die Belastbarkeitsgrenzen ökologischer Systeme zu überschreiten, nur durch wissenschaftlichen Fortschritt bewältigt werden (Abb. 1), der eine nachhaltige und ressourcen­effiziente Steigerung der Agrarproduktion ermöglicht (FAO, 2011; Dobermann und Nelson, 2013). Die nachhaltige Intensivierung stellt die Agrarwissenschaften vor neue Aufgaben, die weit über ihre klassischen Grenzen hinausgehen.Die Senatskommission plädiert daher für eine Erweiterung der agrarwissenschaftlichen Perspektive. Die meist auf einzelne Feldfrüchte bezogene Bewertung der Rela­tion zwischen Input und Ertrag muss ergänzt werden um die Optionen, die sich aus der räumlichen und zeitlichen Diversifikation der Produktionssysteme unter Einbeziehung der standörtlichen Eigenschaften, des Landschaftskontextes sowie des Klimawandels ergeben. Um Ökosystemleistungen einzubeziehen, müssen Produktionsstrategien entwickelt werden, die sich auf ganze Landschaften und Regionen richten und auch entsprechende sozio­öko­no­mische und agrarpolitische Rahmenbedingungen berücksichtigen.Vor diesem Hintergrund schlägt die Senatskommission drei interdisziplinäre Forschungsschwerpunkte zur ressourceneffizienten Erhöhung der Flächenproduktivität vor:(1) Ausnutzung des Potentials von Kulturpflanzen zur umweltschonenden Ertragssteigerung im Kontext öko­systemarer Bedingungen.(2) Nachhaltige Steigerung der Pflanzenproduktion im Landschaftskontext.(3) Ökonomische, gesellschaftliche und politische Dimensionen der Ertragssteigerung von Kulturpflanzen. DOI: 10.5073/JfK.2014.07.01, https://doi.org/10.5073/JfK.2014.07.01With its policy paper the Senate Commission on Agro-ecosystem Research of the Deutsche Forschungsgemeinschaft (DFG) summarizes potential benefits of basic research for the sustainable intensification of crop production. Agro-ecosystems critically contribute to fulfilling the need for increasing food and fiber production, diminishing resource depletion as well as counteracting biodiversity loss and climate change. Yield demands that are needed to ensure the food supply predicted for the year 2050 can only be achieved by scientific progress that allows the intensive yet environmentally friendly production of plant biomass (Figure 1), (FAO, 2011; Dobermann und Nelson, 2013; Ray et al., 2013). Sustainable intensification requires a scientific realignment that allows for broadening the scope of agricultural research. The productivity of farming systems should be evaluated with regard to their efficiency (input-output relation). In addition, the spatial and temporal variability of these systems must be considered by addressing local conditions, the landscape context and climate change. With respect to ecosystem services, new production strategies must be developed that take all aspects of landscape and regional complexity as well as socio-economic conditions and agricultural policy into account.Against this background, the Senate Commission on Agro-ecosystem Research proposes three priority areas of interdisciplinary research on resource efficient intensification of crop production:(1) Exploiting the biological potential of the individual crop plants for an environmentally friendly intensification in an ecosystem approach(2) Exploring sustainable intensification of crop production within a landscape context(3) Taking full account of the economic, social and political dimensions of sustainable intensification of crop production DOI: 10.5073/JfK.2014.07.01, https://doi.org/10.5073/JfK.2014.07.0

Low-Dimensional Palladium Nanostructures for Fast and Reliable Hydrogen Gas Detection

Palladium (Pd) has received attention as an ideal hydrogen sensor material due to its properties such as high sensitivity and selectivity to hydrogen gas, fast response, and operability at room temperature. Interestingly, various Pd nanostructures that have been realized by recent developments in nanotechnologies are known to show better performance than bulk Pd. This review highlights the characteristic properties, issues, and their possible solutions of hydrogen sensors based on the low-dimensional Pd nanostructures with more emphasis on Pd thin films and Pd nanowires. The finite size effects, relative strengths and weaknesses of the respective Pd nanostructures are discussed in terms of performance, manufacturability, and practical applicability

Predicting haplogroups using a versatile machine learning program (PredYMaLe) on a new mutationally balanced 32 Y-STR multiplex (CombYplex): Unlocking the full potential of the human STR mutation rate spectrum to estimate forensic parameters

We developed a new mutationally well-balanced 32 Y-STR multiplex (CombYplex) together with a machine learning (ML) program PredYMaLe to assess the impact of STR mutability on haplogourp prediction, while respecting forensic community criteria (high DC/HD). We designed CombYplex around two sub-panels M1 and M2 characterized by average and high-mutation STR panels. Using these two sub-panels, we tested how our program PredYmale reacts to mutability when considering basal branches and, moving down, terminal branches. We tested first the discrimination capacity of CombYplex on 996 human samples using various forensic and statistical parameters and showed that its resolution is sufficient to separate haplogroup classes. In parallel, PredYMaLe was designed and used to test whether a ML approach can predict haplogroup classes from Y-STR profiles. Applied to our kit, SVM and Random Forest classifiers perform very well (average 97 %), better than Neural Network (average 91 %) and Bayesian methods (< 90 %)

Longitudinal relationship between human papillomavirus infection and the incidence and progression of precursor lesions of cervical neoplasia

Introduction. Human papillomavirus (HPV) infection is now believed to be the central cause of cervical cancer. However, most of the epidemiological evidence has come from retrospective, case-control studies, which do not provide information on the dynamics of a cumulative or persistent HPV infection.Objectives. (1) To measure the risk of incident neoplastic cervical lesions over time related to prior cumulative and persistent HPV infections. (2) To evaluate the influence of HPV viral burden on lesion risk longitudinally. (3) To estimate the progression rates and sojourn time for precursor squamous intraepithelial lesions (SILs) and how they relate to HPV infection status.Design and methods. In 1993, the Ludwig-McGill study team began a large longitudinal study of the natural history of HPV infection and cervical neoplasia in the city of Sao Paulo, Brazil. Follow-up involved repeated measurements on individual subjects over time. 2462 women were enrolled into the study and were seen every 4 months in the first year (0, 4, 8 and 12 months), and twice yearly thereafter for a period of up to eight years. In addition to obtaining risk factor information via questionnaire, cervical specimens were taken for Pap cytology and HPV testing at every visit. Statistical analyses entailed: (1) using different modalities for defining HPV persistence by type and intensity; (2) using modeling approaches that take into account the repeated measurements of HPV and SIL over time within individuals; (3) analyzing changes in transition states between different cervical lesion grades and the rate of progression from one state to the next.Rationale. A longitudinal, repeated measurement cohort investigation, such as this one, permits an accurate and unbiased assessment of the relationship between cumulative HPV exposure and lesion incidence. An elevated relationship between persistent HPV infections and SIL incidence supports the proposal for the application of type-specific molecular HPV DNA testing as a screening tool for the detection of cervical neoplasia. Better understanding of the natural history of disease can help in developing effective and efficient public health programs in prevention for cervical cancer