Testing the performance of environmental DNA metabarcoding for surveying highly diverse tropical fish communities: A case study from Lake Tanganyika

Background and Aims Environmental DNA (eDNA) metabarcoding provides a highly sensitive method of surveying freshwater fish communities, although studies to date have largely been restricted to temperate ecosystems. Due to limited reference sequence availability and challenges identifying closely related and rare species in diverse tropical ecosystems, the effectiveness of metabarcoding methods for surveying tropical fish communities from eDNA samples remains uncertain. To address this, we applied an eDNA metabarcoding approach to survey Lake Tanganyika's (LT) species‐rich littoral fish communities. Materials and Methods As this system contains many closely related species, particularly cichlid fishes, we used four primer sets including a cichlid‐specific primer set (Cichlid_CR). A reference database was built for the 12s, 16s, and control region for 358 fish species including over 93% of known cichlids. Results and Discussion In silico and in situ results demonstrated wide variability in the taxonomic resolution of assignments by each primer with the cichlid‐specific marker (Cichlid_CR) enabling greater species‐level assignments for this highly diverse family. A greater number of non‐cichlid teleost species were detected at sites compared to the visual survey data. For cichlid species however, sequencing depth substantially influenced species richness estimates obtained from eDNA samples, with increased depths producing estimates comparable to that obtained from the visual survey data. Conclusions Our study highlights the importance of sequencing depth and local reference databases when undertaking metabarcoding studies within diverse ecosystems, as well as demonstrating the potential of eDNA metabarcoding for surveying diverse tropical fish communities, even those containing closely related species within evolutionary radiations

The resultant on compact Riemann surfaces

We introduce a notion of resultant of two meromorphic functions on a compact Riemann surface and demonstrate its usefulness in several respects. For example, we exhibit several integral formulas for the resultant, relate it to potential theory and give explicit formulas for the algebraic dependence between two meromorphic functions on a compact Riemann surface. As a particular application, the exponential transform of a quadrature domain in the complex plane is expressed in terms of the resultant of two meromorphic functions on the Schottky double of the domain.Comment: 44 page

Polarization transfer in the 4^{4}He(e⃗,e′p⃗3(\vec{e},e' \vec{p}^{3}H reaction

Polarization transfer in the 4He(e,e'p)3H reaction at a Q^2 of 0.4 (GeV/c)^2 was measured at the Mainz Microtron MAMI. The ratio of the transverse to the longitudinal polarization components of the ejected protons was compared with the same ratio for elastic ep scattering. The results are consistent with a recent fully relativistic calculation which includes a predicted medium modification of the proton form factor based on a quark-meson coupling model.Comment: 5 pages, Latex, 2 postscript figures, submitted to Physics Letters

Inclusive electron scattering in a relativistic Green function approach

A relativistic Green function approach to the inclusive quasielastic (e,e') scattering is presented. The single particle Green function is expanded in terms of the eigenfunctions of the nonhermitian optical potential. This allows one to treat final state interactions consistently in the inclusive and in the exclusive reactions. Numerical results for the response functions and the cross sections for different target nuclei and in a wide range of kinematics are presented and discussed in comparison with experimental data.Comment: 12 pages, 7 figures, REVTeX

Coherent control of electron spin qubits in silicon using a global field

Silicon spin qubits promise to leverage the extraordinary progress in silicon nanoelectronic device fabrication over the past half century to deliver large-scale quantum processors. Despite the scalability advantage of using silicon technology, realising a quantum computer with the millions of qubits required to run some of the most demanding quantum algorithms poses several outstanding challenges, including how to control many qubits simultaneously. Recently, compact 3D microwave dielectric resonators were proposed as a way to deliver the magnetic fields for spin qubit control across an entire quantum chip using only a single microwave source. Although spin resonance of individual electrons in the globally applied microwave field was demonstrated, the spins were controlled incoherently. Here we report coherent Rabi oscillations of single electron spin qubits in a planar SiMOS quantum dot device using a global magnetic field generated off-chip. The observation of coherent qubit control driven by a dielectric resonator establishes a credible pathway to achieving large-scale control in a spin-based quantum computer

Relativistic Structure of the Deuteron: 1.Electro-disintegration and y-scaling

Realistic solutions of the spinor-spinor Bethe-Salpeter equation for the deuteron with realistic interaction kernel including the exchange of pi, sigma, omega, rho, eta and delta mesons, are used to systematically investigate relativistic effects in inclusive quasi-elastic electron-deuteron scattering within the relativistic impulse approximation. Relativistic y-scaling is considered by generalising the non relativistic scaling function to the relativistic case, and it is shown that y-scaling does occur in the usual relativistic scaling variable resulting from the energy conservation in the instant form of dynamics. The present approach of y-scaling is fully covariant, with the deuteron being described by eight components, viz. the 3S_1^{++}, 3S_1^{--}, 3D_1^{++}, 3D_1^{--}, 3P_1^{+-}, 3P_1^{-+}, 1P_1^{+-}, 1P_1^{-+} waves. It is demonstrated that if the negative relative energy states 1P_1, 3P_1 are disregarded, the concept of covariant momentum distributions N(p_0,p), with p_0=M_D/2-\sqrt{p^2+m^2}, can be introduced, and that calculations of lectro-disintegration cross section in terms of these distributions agree within few percents with the exact calculations which include the 1P_1, 3P_1 states, provided the nucleon three momentum |p|\<= 1 GeV/c; in this momentum range, the asymptotic relativistic scaling function is shown to coincide with the longitudinal covariant momentum distribution.Comment: 32 LaTeX pages, 18 eps-figures. Final version to appear in Phys. Rev.

Computational Nuclear Physics and Post Hartree-Fock Methods

We present a computational approach to infinite nuclear matter employing Hartree-Fock theory, many-body perturbation theory and coupled cluster theory. These lectures are closely linked with those of chapters 9, 10 and 11 and serve as input for the correlation functions employed in Monte Carlo calculations in chapter 9, the in-medium similarity renormalization group theory of dense fermionic systems of chapter 10 and the Green's function approach in chapter 11. We provide extensive code examples and benchmark calculations, allowing thereby an eventual reader to start writing her/his own codes. We start with an object-oriented serial code and end with discussions on strategies for porting the code to present and planned high-performance computing facilities.Comment: 82 pages, to appear in Lecture Notes in Physics (Springer), "An advanced course in computational nuclear physics: Bridging the scales from quarks to neutron stars", M. Hjorth-Jensen, M. P. Lombardo, U. van Kolck, Editor

Neutron structure function and inclusive DIS from H-3 and He-3 at large Bjorken-x

A detailed study of inclusive deep inelastic scattering (DIS) from mirror A = 3 nuclei at large values of the Bjorken variable x is presented. The main purpose is to estimate the theoretical uncertainties on the extraction of the neutron DIS structure function from such nuclear measurements. On one hand, within models in which no modification of the bound nucleon structure functions is taken into account, we have investigated the possible uncertainties arising from: i) charge symmetry breaking terms in the nucleon-nucleon interaction, ii) finite Q**2 effects neglected in the Bjorken limit, iii) the role of different prescriptions for the nucleon Spectral Function normalization providing baryon number conservation, and iv) the differences between the virtual nucleon and light cone formalisms. Although these effects have been not yet considered in existing analyses, our conclusion is that all these effects cancel at the level of ~ 1% for x < 0.75 in overall agreement with previous findings. On the other hand we have considered several models in which the modification of the bound nucleon structure functions is accounted for to describe the EMC effect in DIS scattering from nuclei. It turns out that within these models the cancellation of nuclear effects is expected to occur only at a level of ~ 3%, leading to an accuracy of ~ 12 % in the extraction of the neutron to proton structure function ratio at x ~ 0.7 -0.8$. Another consequence of considering a broad range of models of the EMC effect is that the previously suggested iteration procedure does not improve the accuracy of the extraction of the neutron to proton structure function ratio.Comment: revised version to appear in Phys. Rev. C; main modifications in Section 4; no change in the conclusion

Effects of Cooking in Solutions of Varying pH on the Dietary Fiber Components of Vegetables

To study the effect of pH on dietary fiber components of vegetables, beans, cauliflower, potatoes, peas and corn were cooked in buffers of pH 2, 4, 6, and 10. Water-soluble pectin and hemicellulose, water-insoluble pectin and hemicellulose, cellulose and lignin were quantitated in raw, cooked vegetables and cooking medium. Tenderness and pH of raw and cooked vegetables were determined. Texture varied with cooking medium. Cooked vegetables were most firm at pH 4 and softest at pH 10. Dietary components found in cooking medium reflected these textural changes. Vegetables which showed greater pH effects exhibited greater changes in fiber components.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/73821/1/j.1365-2621.1984.tb13237.x.pd

Investigating magmatic processes in the early Solar System using the Cl isotopic systematics of eucrites

Generally, terrestrial rocks, martian and chondritic meteorites exhibit a relatively narrow range in bulk and apatite Cl isotope compositions, with δ37Cl (per mil deviation from standard mean ocean chloride) values between − 5.6 and + 3.8 ‰. Lunar rocks, however, have more variable bulk and apatite δ37Cl values, ranging from ∼ − 4 to + 40 ‰. As the Howardite-Eucrite-Diogenite (HED) meteorites represent the largest suite of crustal and sub-crustal rocks available from a differentiated basaltic asteroid (4 Vesta), studying them for their volatiles may provide insights into planetary differentiation processes during the earliest Solar System history. Here the abundance and isotopic composition of Cl in apatite were determined for seven eucrites representing a broad range of textural and petrological characteristics. Apatite Cl abundances range from ∼ 25 to 4900 ppm and the δ37Cl values range from − 3.98 to + 39.2 ‰. Samples with lower apatite H2O contents were typically also enriched in 37Cl but no systematic correlation between δ37Cl and δD values was observed across samples. Modelled Rayleigh fractionation and a strong positive correlation between bulk δ66Zn and apatite δ37Cl support the hypothesis that Cl degassed as metal chlorides from eucritic magmas, in a hydrogen-poor environment. In the case of lunar samples, it has been noted that δ37Cl values of apatite positively correlate with bulk La/Yb ratio. Interestingly, most eucrites show a negative correlation with bulk La/Yb ratio. Recently, isotopically light Cl values have been suggested to record the primary solar nebular signature. If this is the case then 4 Vesta, which accreted rapidly and early in Solar System history, could also record this primary nebular signature corresponding to the lightest Cl values measured here. The significant variation in Cl isotope composition observed within the eucrites are likely related to degassing of metal chlorides