Three-body description of direct nuclear reactions: Comparison with the continuum discretized coupled channels method

The continuum discretized coupled channels (CDCC) method is compared to the exact solution of the three-body Faddeev equations in momentum space. We present results for: i) elastic and breakup observables of d-12C at E_d=56 MeV, ii) elastic scattering of d-58Ni at E_d=80 MeV, and iii) elastic, breakup and transfer observables for 11Be+p at E_{11Be}/A=38.4 MeV. Our comparative studies show that, in the first two cases, the CDCC method is a good approximation to the full three-body Faddeev solution, but for the 11Be exotic nucleus, depending on the observable or the kinematic regime, it may miss out some of the dynamic three-body effects that appear through the explicit coupling to the transfer channel.Comment: 12 pages, 10 figures, accepted for publication in Physical Review

Noncommutative Quantum Mechanics and rotating frames

We study the effect of noncommutativity of space on the physics of a quantum interferometer located in a rotating disk in a gauge field background. To this end, we develop a path-integral approach which allows defining an effective action from which relevant physical quantities can be computed as in the usual commutative case. For the specific case of a constant magnetic field, we are able to compute, exactly, the noncommutative Lagrangian and the associated shift on the interference pattern for any value of $\theta$.Comment: 17 pages, presentation improved, references added. To appear in Physical Review

General relativistic corrections to the Sagnac effect

The difference in travel time of corotating and counter-rotating light waves in the field of a central massive and spinning body is studied. The corrections to the special relativistic formula are worked out in a Kerr field. Estimation of numeric values for the Earth and satellites in orbit around it show that a direct measurement is in the order of concrete possibilities.Comment: REVTex, accepted for publication on Phys. Rev.

Simultaneity and generalized connections in general relativity

Stationary extended frames in general relativity are considered. The requirement of stationarity allows to treat the spacetime as a principal fiber bundle over the one-dimensional group of time translations. Over this bundle a connection form establishes the simultaneity between neighboring events accordingly with the Einstein synchronization convention. The mathematics involved is that of gauge theories where a gauge choice is interpreted as a global simultaneity convention. Then simultaneity in non-stationary frames is investigated: it turns to be described by a gauge theory in a fiber bundle without structure group, the curvature being given by the Fr\"olicher-Nijenhuis bracket of the connection. The Bianchi identity of this gauge theory is a differential relation between the vorticity field and the acceleration field. In order for the simultaneity connection to be principal, a necessary and sufficient condition on the 4-velocity of the observers is given.Comment: RevTeX, 9 pages, 2 figures, 1 table. Previous title "The gauge nature of simultaneity". Classical and Quantum Gravity http://www.iop.org/EJ/journal/CQ

Deuteron Elastic-Scattering at 110 and 120 Mev

Journals published by the American Physical Society can be found at http://publish.aps.org/Deuteron elastic scattering cross sections have been measured at 110 and 120 MeV on C, Ni-58, and Pb-208. Optical model potentials have been extracted and compared to deuteron global optical model potentials

Renormalization of the weak hadronic current in the nuclear medium

The renormalization of the weak charge-changing hadronic current as a function of the reaction energy release is studied at the nucleonic level. We have calculated the average quenching factors for each type of current (vector, axial vector and induced pseudoscalar). The obtained quenching in the axial vector part is, at zero momentum transfer, 19% for the sd shell and 23% in the fp shell. We have extended the calculations also to heavier systems such as $^{56}$Ni and $^{100}$Sn, where we obtain stronger quenchings, 44% and 59%, respectively. Gamow--Teller type transitions are discussed, along with the higher order matrix elements. The quenching factors are constant up to roughly 60 MeV momentum transfer. Therefore the use of energy-independent quenching factors in beta decay is justified. We also found that going beyond the zeroth and first order operators (in inverse nucleon mass) does not give any substantial contribution. The extracted renormalization to the ratio $C_P/C_A$ at q=100 MeV is -3.5%, -7.1$%, -28.6%, and +8.7% for mass 16, 40, 56, and 100, respectively.Comment: 28 pages, 6 figure

African Rice (Oryza glaberrima Steud.): Lost Crop of the Enslaved Africans Discovered in Suriname1

African Rice (Oryza glaberrimaSteud.): Lost Crop of the Enslaved Africans Discovered in Suriname. African rice (Oryza glaberrima Steud.) was introduced to the Americas during the slave trade years and grown by enslaved Africans for decades before mechanical milling devices facilitated the shift towards Asian rice (O. sativa L.). Literature suggests that African rice is still grown in Guyana and French Guiana, but the most recent herbarium voucher dates from 1938. In this paper, evidence is presented that O. glaberrima is still grown by Saramaccan Maroons both for food and ritual uses. Saramaccan informants claim their forefathers collected their first “black rice” from a mysterious wild rice swamp and cultivated these seeds afterwards. Unmilled spikelets (grains with their husk still attached) are sold in small quantities for ancestor offerings, and even exported to the Netherlands to be used by Maroon immigrants. Little is known of the evolution of O. glaberrima, before and after domestication. Therefore, more research is needed on the different varieties of rice and other “lost crops” grown by these descendants of enslaved Africans who escaped from plantations in the 17th and 18th centuries and maintained much of their African cultural heritage in the deep rainforest

MultiMSOAR 2.0: An Accurate Tool to Identify Ortholog Groups among Multiple Genomes

The identification of orthologous genes shared by multiple genomes plays an important role in evolutionary studies and gene functional analyses. Based on a recently developed accurate tool, called MSOAR 2.0, for ortholog assignment between a pair of closely related genomes based on genome rearrangement, we present a new system MultiMSOAR 2.0, to identify ortholog groups among multiple genomes in this paper. In the system, we construct gene families for all the genomes using sequence similarity search and clustering, run MSOAR 2.0 for all pairs of genomes to obtain the pairwise orthology relationship, and partition each gene family into a set of disjoint sets of orthologous genes (called super ortholog groups or SOGs) such that each SOG contains at most one gene from each genome. For each such SOG, we label the leaves of the species tree using 1 or 0 to indicate if the SOG contains a gene from the corresponding species or not. The resulting tree is called a tree of ortholog groups (or TOGs). We then label the internal nodes of each TOG based on the parsimony principle and some biological constraints. Ortholog groups are finally identified from each fully labeled TOG. In comparison with a popular tool MultiParanoid on simulated data, MultiMSOAR 2.0 shows significantly higher prediction accuracy. It also outperforms MultiParanoid, the Roundup multi-ortholog repository and the Ensembl ortholog database in real data experiments using gene symbols as a validation tool. In addition to ortholog group identification, MultiMSOAR 2.0 also provides information about gene births, duplications and losses in evolution, which may be of independent biological interest. Our experiments on simulated data demonstrate that MultiMSOAR 2.0 is able to infer these evolutionary events much more accurately than a well-known software tool Notung. The software MultiMSOAR 2.0 is available to the public for free

MSOAR 2.0: Incorporating tandem duplications into ortholog assignment based on genome rearrangement

<p>Abstract</p> <p>Background</p> <p>Ortholog assignment is a critical and fundamental problem in comparative genomics, since orthologs are considered to be functional counterparts in different species and can be used to infer molecular functions of one species from those of other species. MSOAR is a recently developed high-throughput system for assigning one-to-one orthologs between closely related species on a genome scale. It attempts to reconstruct the evolutionary history of input genomes in terms of genome rearrangement and gene duplication events. It assumes that a gene duplication event inserts a duplicated gene into the genome of interest at a random location (<it>i.e.</it>, the random duplication model). However, in practice, biologists believe that genes are often duplicated by tandem duplications, where a duplicated gene is located next to the original copy (<it>i.e.</it>, the tandem duplication model).</p> <p>Results</p> <p>In this paper, we develop MSOAR 2.0, an improved system for one-to-one ortholog assignment. For a pair of input genomes, the system first focuses on the tandemly duplicated genes of each genome and tries to identify among them those that were duplicated after the speciation (<it>i.e.</it>, the so-called inparalogs), using a simple phylogenetic tree reconciliation method. For each such set of tandemly duplicated inparalogs, all but one gene will be deleted from the concerned genome (because they cannot possibly appear in any one-to-one ortholog pairs), and MSOAR is invoked. Using both simulated and real data experiments, we show that MSOAR 2.0 is able to achieve a better sensitivity and specificity than MSOAR. In comparison with the well-known genome-scale ortholog assignment tool InParanoid, Ensembl ortholog database, and the orthology information extracted from the well-known whole-genome multiple alignment program MultiZ, MSOAR 2.0 shows the highest sensitivity. Although the specificity of MSOAR 2.0 is slightly worse than that of InParanoid in the real data experiments, it is actually better than that of InParanoid in the simulation tests.</p> <p>Conclusions</p> <p>Our preliminary experimental results demonstrate that MSOAR 2.0 is a highly accurate tool for one-to-one ortholog assignment between closely related genomes. The software is available to the public for free and included as online supplementary material.</p

Outcome After Surgical Stabilization of Rib Fractures Versus Nonoperative Treatment in Patients With Multiple Rib Fractures and Moderate to Severe Traumatic Brain Injury (CWIS-TBI)

BACKGROUND Outcomes after surgical stabilization of rib fractures (SSRF) have not been studied in patients with multiple rib fractures and traumatic brain injury (TBI). We hypothesized that SSRF, as compared with nonoperative management, is associated with favorable outcomes in patients with TBI. METHODS A multicenter, retrospective cohort study was performed in patients with rib fractures and TBI between January 2012 and July 2019. Patients who underwent SSRF were compared to those managed nonoperatively. The primary outcome was mechanical ventilation-free days. Secondary outcomes were intensive care unit length of stay and hospital length of stay, tracheostomy, occurrence of complications, neurologic outcome, and mortality. Patients were further stratified into moderate (GCS score, 9–12) and severe (GCS score, ≤8) TBI. RESULTS The study cohort consisted of 456 patients of which 111 (24.3%) underwent SSRF. The SSRF was performed at a median of 3 days, and SSRF-related complication rate was 3.6%. In multivariable analyses, there was no difference in mechanical ventilation-free days between the SSRF and nonoperative groups. The odds of developing pneumonia (odds ratio [OR], 0.59; 95% confidence interval [95% CI], 0.38–0.98; p = 0.043) and 30-day mortality (OR, 0.32; 95% CI, 0.11–0.91; p = 0.032) were significantly lower in the SSRF group. Patients with moderate TBI had similar outcome in both groups. In patients with severe TBI, the odds of 30-day mortality was significantly lower after SSRF (OR, 0.19; 95% CI, 0.04–0.88; p = 0.034). CONCLUSION In patients with multiple rib fractures and TBI, the mechanical ventilation-free days did not differ between the two treatment groups. In addition, SSRF was associated with a significantly lower risk of pneumonia and 30-day mortality. In patients with moderate TBI, outcome was similar. In patients with severe TBI a lower 30-day mortality was observed. There was a low SSRF-related complication risk. These data suggest a potential role for SSRF in select patients with TBI. LEVEL OF EVIDENCE Therapeutic, level IV