No alignment of cattle along geomagnetic field lines found

This paper presents a study of the body orientation of domestic cattle on free pastures in several European states, based on Google satellite photographs. In sum, 232 herds with 3412 individuals were evaluated. Two independent groups participated in our study and came to the same conclusion that, in contradiction to the recent findings of other researchers, no alignment of the animals and of their herds along geomagnetic field lines could be found. Several possible reasons for this discrepancy should be taken into account: poor quality of Google satellite photographs, difficulties in determining the body axis, selection of herds or animals within herds, lack of blinding in the evaluation, possible subconscious bias, and, most importantly, high sensitivity of the calculated main directions of the Rayleigh vectors to some kind of bias or to some overlooked or ignored confounder. This factor could easily have led to an unsubstantiated positive conclusion about the existence of magnetoreception.Comment: Added electronic supplement with source dat

Operational experience, improvements, and performance of the CDF Run II silicon vertex detector

The Collider Detector at Fermilab (CDF) pursues a broad physics program at Fermilab's Tevatron collider. Between Run II commissioning in early 2001 and the end of operations in September 2011, the Tevatron delivered 12 fb-1 of integrated luminosity of p-pbar collisions at sqrt(s)=1.96 TeV. Many physics analyses undertaken by CDF require heavy flavor tagging with large charged particle tracking acceptance. To realize these goals, in 2001 CDF installed eight layers of silicon microstrip detectors around its interaction region. These detectors were designed for 2--5 years of operation, radiation doses up to 2 Mrad (0.02 Gy), and were expected to be replaced in 2004. The sensors were not replaced, and the Tevatron run was extended for several years beyond its design, exposing the sensors and electronics to much higher radiation doses than anticipated. In this paper we describe the operational challenges encountered over the past 10 years of running the CDF silicon detectors, the preventive measures undertaken, and the improvements made along the way to ensure their optimal performance for collecting high quality physics data. In addition, we describe the quantities and methods used to monitor radiation damage in the sensors for optimal performance and summarize the detector performance quantities important to CDF's physics program, including vertex resolution, heavy flavor tagging, and silicon vertex trigger performance.Comment: Preprint accepted for publication in Nuclear Instruments and Methods A (07/31/2013

Pauli's Principle in Probe Microscopy

Exceptionally clear images of intramolecular structure can be attained in dynamic force microscopy through the combination of a passivated tip apex and operation in what has become known as the "Pauli exclusion regime" of the tip-sample interaction. We discuss, from an experimentalist's perspective, a number of aspects of the exclusion principle which underpin this ability to achieve submolecular resolution. Our particular focus is on the origins, history, and interpretation of Pauli's principle in the context of interatomic and intermolecular interactions.Comment: This is a chapter from "Imaging and Manipulation of Adsorbates using Dynamic Force Microscopy", a book which is part of the "Advances in Atom and Single Molecule Machines" series published by Springer [http://www.springer.com/series/10425]. To be published late 201

Bacterial Distribution in the Rhizosphere of Wild Barley under Contrasting Microclimates

Background: All plants in nature harbor a diverse community of rhizosphere bacteria which can affect the plant growth. Our samples are isolated from the rhizosphere of wild barley Hordeum spontaneum at the Evolution Canyon (‘EC’), Israel. The bacteria which have been living in close relationship with the plant root under the stressful conditions over millennia are likely to have developed strategies to alleviate plant stress. Methodology/Principal Findings: We studied distribution of culturable bacteria in the rhizosphere of H. spontaneum and characterized the bacterial 1-aminocyclopropane-1-carboxylate deaminase (ACCd) production, biofilm production, phosphorus solubilization and halophilic behavior. We have shown that the H. spontaneum rhizosphere at the stressful South Facing Slope (SFS) harbors significantly higher population of ACCd producing biofilm forming phosphorus solubilizing osmotic stress tolerant bacteria. Conclusions/Significance: The long-lived natural laboratory ‘EC ’ facilitates the generation of theoretical testable and predictable models of biodiversity and genome evolution on the area of plant microbe interactions. It is likely that the bacteria isolated at the stressful SFS offer new opportunities for the biotechnological applications in our agro-ecologica

Fermilab Main Injector Beam Position Monitor Upgrade

An upgrade of the Beam Position Monitor (BPM) signal processing and data acquisition system for the Fermilab Main Injector is described. The Main Injector is a fast cycling synchrotron that accelerates protons or antiprotons from 8 to 150 GeV. Each Main Injector cycle can have a totally different magnet ramp, RF frequency configuration, beam bunch structure, and injection/extraction pattern from the previous cycle. The new BPM system provides the capabilities and flexibility required by the dynamic and complex machine operations. The system offers measurement capability in the 2.5 MHz and 53 MHz channels to detect the range of bunch structures for protons and antiprotons in both wideband (turn-by-turn) and narrowband (closed-orbit) modes. The new BPM read-out system is based on the digital receiver concept and is highly configurable, allowing the signal processing of nearly all Main Injector beam conditions, including the detection of individual batches. An overview of the BPM system in the Main Injector operating environment, some technology details and first beam measurements are presented

Burst of Young Retrogenes and Independent Retrogene Formation in Mammals

Retroposition and retrogenes gain increasing attention as recent studies show that they play an important role in human new gene formation. Here we examined the patterns of retrogene distribution in 8 mammalian genomes using 4 non-mammalian genomes as a contrast. There has been a burst of young retrogenes not only in primate lineages as suggested in a recent study, but also in other mammalian lineages. In mammals, most of the retrofamilies (the gene families that have retrogenes) are shared between species. In these shared retrofamilies, 14%–18% of functional retrogenes may have originated independently in multiple mammalian species. Notably, in the independently originated retrogenes, there is an enrichment of ribosome related gene function. In sharp contrast, none of these patterns hold in non-mammals. Our results suggest that the recruitment of the specific L1 retrotransposons in mammals might have been an important evolutionary event for the split of mammals and non-mammals and retroposition continues to be an important active process in shaping the dynamics of mammalian genomes, as compared to being rather inert in non-mammals