Non-Hermitian matter-wave mixing in Bose-Einstein condensates: Dissipation-induced amplification

We investigate the nonlinear scattering dynamics in interacting atomic Bose-Einstein condensates under non-Hermitian dissipative conditions. We show that, by carefully engineering a momentum-dependent atomic loss profile, one can achieve matter-wave amplification through four-wave mixing in a quasi-one-dimensional nearly-free-space setup—a process that is forbidden in the counterpart Hermitian systems due to energy mismatch. Additionally, we show that similar effects lead to rich nonlinear dynamics in higher dimensions. Finally, we propose a physical realization for selectively tailoring the momentum-dependent atomic dissipation. Our strategy is based on a two-step process: (i) exciting atoms to narrow Rydberg or metastable excited states, and (ii) introducing loss through recoil; all while leaving the bulk condensate intact due to protection by quantum interference

Correlations of Rydberg excitations in an ultra-cold gas after an echo sequence

We show that Rydberg states in an ultra-cold gas can be excited with strongly preferred nearest-neighbor distance if densities are well below saturation. The scheme makes use of an echo sequence in which the first half of a laser pulse excites Rydberg states while the second half returns atoms to the ground state, as in the experiment of Raitzsch et al. [Phys. Rev. Lett. 100 (2008) 013002]. Near to the end of the echo sequence, almost any remaining Rydberg atom is separated from its next-neighbor Rydberg atom by a distance slightly larger than the instantaneous blockade radius half-way through the pulse. These correlations lead to large deviations of the atom counting statistics from a Poissonian distribution. Our results are based on the exact quantum evolution of samples with small numbers of atoms. We finally demonstrate the utility of the omega-expansion for the approximate description of correlation dynamics through an echo sequence.Comment: 8 pages, 6 figure

Fangs for the Memories? A Survey of Pain in Snakebite Patients Does Not Support a Strong Role for Defense in the Evolution of Snake Venom Composition

Animals use venoms for multiple purposes, most prominently for prey acquisition and self-defense. In snakes, venom composition often evolves as a result of selection for optimization for local diet. However, whether selection for a defensive function has also played a role in driving the evolution of venom composition has remained largely unstudied. Here, we use an online survey of snakebite victims to test a key prediction of a defensive function, that envenoming should result in the rapid onset of severe pain. From the analysis of 584 snakebite reports, involving 192 species of venomous snake, we find that the vast majority of bites do not result in severe early pain. Phylogenetic comparative analysis shows that where early pain after a bite evolves, it is often lost rapidly. Our results, therefore, do not support the hypothesis that natural selection for antipredator defense played an important role in the origin of venom or front-fanged delivery systems in general, although there may be intriguing exceptions to this rule

Spial: analysis of subtype-specific features in multiple sequence alignments of proteins

Motivation: Spial (Specificity in alignments) is a tool for the comparative analysis of two alignments of evolutionarily related sequences that differ in their function, such as two receptor subtypes. It highlights functionally important residues that are either specific to one of the two alignments or conserved across both alignments. It permits visualization of this information in three complementary ways: by colour-coding alignment positions, by sequence logos and optionally by colour-coding the residues of a protein structure provided by the user. This can aid in the detection of residues that are involved in the subtype-specific interaction with a ligand, other proteins or nucleic acids. Spial may also be used to detect residues that may be post-translationally modified in one of the two sets of sequences. Availability: http://www.mrc-lmb.cam.ac.uk/genomes/spial/; supplementary information is available at http://www.mrc-lmb.cam.ac.uk/genomes/spial/help.html Contact: [email protected]

Fano resonances in quantum transport with vibrations

Quantum-mechanical scattering involving continuum states coupled to a scatterer with a discrete spectrum gives rise to Fano resonances. Here we consider scatterers that possess internal vibrational degrees of freedom in addition to discrete states. Entanglement between the scattered excitation and vibrational modes complicates analytical and numerical calculations considerably. For the example of one-dimensional scattering we develop a multichannel quantum scattering approach which can determine reflection and transmission probabilities in the presence of vibrations. Application to a linear chain coupled to a control unit containing vibrating sites shows that vibrational degrees of freedom can have a profound effect on quantum transport. For suitable parameters, spectral regions which are opaque in the static case can be rendered transparent when vibrations are included. The formalism is general enough to be applicable to a variety of platforms for quantum transport including molecular aggregates, cold atom chains, quantum-dot arrays and molecular wires based on conjugated polymers

Cells alter their tRNA abundance to selectively regulate protein synthesis during stress conditions

Decoding the information in mRNA during protein synthesis relies on tRNA adaptors, the abundance of which can affect the decoding rate and translation efficiency. To determine whether cells alter tRNA abundance to selectively regulate protein expression, we quantified changes in the abundance of individual tRNAs at different time points in response to diverse stress conditions in Saccharomyces cerevisiae. We found that the tRNA pool was dynamic and rearranged in a manner that facilitated selective translation of stress-related transcripts. Through genomic analysis of multiple data sets, stochastic simulations, and experiments with designed sequences of proteins with identical amino acids but altered codon usage, we showed that changes in tRNA abundance affected protein expression independently of factors such as mRNA abundance. We suggest that cells alter their tRNA abundance to selectively affect the translation rates of specific transcripts to increase the amounts of required proteins under diverse stress conditions

Primary treatment of acromegaly with high-dose lanreotide: a case series

<p>Abstract</p> <p>Introduction</p> <p>The first-line treatment for acromegaly is transsphenoidal surgery. In approximately 50% of patients, however, a cure is not possible with surgery and alternatives are needed. Somatostatin analog therapy is the recommended first-line treatment in patients with such cases. Here we provide the first report of a high-dose lanreotide primary therapy in patients with acromegaly.</p> <p>Case presentation</p> <p>Six patients who were not suitable for surgery were given 60 mg of lanreotide (Autogel^®) every four weeks. All patients were German nationals and Caucasian.</p> <p>When the response of our patients was unsatisfactory, the dose was increased sequentially to 90 mg every four weeks, 120 mg every four weeks, 120 mg every three weeks and 180 mg every three weeks. Treatment duration was 12 to 24 months. In all cases, the lanreotide dose was 120 mg every 4 weeks or higher. In five of our patients, growth hormone (GH) levels were successfully reduced (in three patients GH <2.5 ng/ml was achieved). Insulin-like growth factor 1 levels were normalized in three patients and decreased in two patients. One patient failed to show a biochemical response to lanreotide therapy or pegvisomant therapy.</p> <p>Tumor shrinkage or degeneration was observed in the five responding patients. No drug-related adverse events were noted.</p> <p>Conclusions</p> <p>These results suggest that lanreotide at high doses of 120 mg every four weeks or more is an effective first-line therapy for patients with acromegaly that surgery alone cannot treat.</p

Phylogeography of the Central American lancehead Bothrops asper (SERPENTES: VIPERIDAE)

The uplift and final connection of the Central American land bridge is considered the major event that allowed biotic exchange between vertebrate lineages of northern and southern origin in the New World. However, given the complex tectonics that shaped Middle America, there is still substantial controversy over details of this geographical reconnection, and its role in determining biogeographic patterns in the region. Here, we examine the phylogeography of Bothrops asper, a widely distributed pitviper in Middle America and northwestern South America, in an attempt to evaluate how the final Isthmian uplift and other biogeographical boundaries in the region influenced genealogical lineage divergence in this species. We examined sequence data from two mitochondrial genes (MT-CYB and MT-ND4) from 111 specimens of B. asper, representing 70 localities throughout the species' distribution. We reconstructed phylogeographic patterns using maximum likelihood and Bayesian methods and estimated divergence time using the Bayesian relaxed clock method. Within the nominal species, an early split led to two divergent lineages of B. asper: one includes five phylogroups distributed in Caribbean Middle America and southwestern Ecuador, and the other comprises five other groups scattered in the Pacific slope of Isthmian Central America and northwestern South America. Our results provide evidence of a complex transition that involves at least two dispersal events into Middle America during the final closure of the Isthmus

Spial: analysis of subtype-specific features in multiple sequence alignments of proteins

Motivation: Spial (Specificity in alignments) is a tool for the comparative analysis of two alignments of evolutionarily related sequences that differ in their function, such as two receptor subtypes. It highlights functionally important residues that are either specific to one of the two alignments or conserved across both alignments. It permits visualization of this information in three complementary ways: by colour-coding alignment positions, by sequence logos and optionally by colour-coding the residues of a protein structure provided by the user. This can aid in the detection of residues that are involved in the subtype-specific interaction with a ligand, other proteins or nucleic acids. Spial may also be used to detect residues that may be post-translationally modified in one of the two sets of sequences