Human-chimpanzee alignment: Ortholog Exponentials and Paralog Power Laws

Genomic subsequences conserved between closely related species such as human and chimpanzee exhibit an exponential length distribution, in contrast to the algebraic length distribution observed for sequences shared between distantly related genomes. We find that the former exponential can be further decomposed into an exponential component primarily composed of orthologous sequences, and a truncated algebraic component primarily composed of paralogous sequences.Comment: Main text: 31 pages, 13 figures, 1 table; Supplementary materials: 9 pages, 9 figures, 1 tabl

Anomalous spin-charge separation in a driven Hubbard system

Spin-charge separation (SCS) is a striking manifestation of strong correlations in low-dimensional quantum systems, whereby a fermion splits into separate spin and charge excitations that travel at different speeds. Here, we demonstrate that periodic driving enables control over SCS in a Hubbard system near half-filling. In one dimension, we predict analytically an exotic regime where charge travels slower than spin and can even become 'frozen', in agreement with numerical calculations. In two dimensions, the driving slows both charge and spin, and leads to complex interferences between single-particle and pair-hopping processes.Comment: arXiv admin note: text overlap with arXiv:2002.0231

Graphic Design Internship

I have always been my own boss. From self-learning graphic design, starting in third grade, to practicing graphic design for clubs and organizations under my digression. I have been lucky enough to work for mainly myself and, when working for others, have had to cater to exclusively my taste—my experience in doing graphic design for teams has in the past been limited to making a design I like, requesting approval with little to no necessary revisions, and finally sending the design to its final destination. Working with the Carbondale Chamber of Commerce this summer was my first time practicing graphic design for someone else. While my personal taste and graphical flare were still appreciated and encouraged, my mentor, LeAnne Gaydos, Program Manager of the Carbondale Chamber of Commerce, called the final shots. This report details my experiences working as a graphic design intern (with a boss) in the midst of the Covid-19 pandemic and its associated restrictions. Below is a table of contents of sorts to acquaint you with this report.https://digitalcommons.imsa.edu/intern_reports_2020/1008/thumbnail.jp

Primary orthologs from local sequence context

BackgroundThe evolutionary history of genes serves as a cornerstone of contemporary biology. Most conserved sequences in mammalian genomes don\u27t code for proteins, yielding a need to infer evolutionary history of sequences irrespective of what kind of functional element they may encode. Thus, sequence-, as opposed to gene-, centric modes of inferring paths of sequence evolution are increasingly relevant. Customarily, homologous sequences derived from the same direct ancestor, whose ancestral position in two genomes is usually conserved, are termed "primary" (or "positional") orthologs. Methods based solely on similarity don\u27t reliably distinguish primary orthologs from other homologs; for this, genomic context is often essential. Context-dependent identification of orthologs traditionally relies on genomic context over length scales characteristic of conserved gene order or whole-genome sequence alignment, and can be computationally intensive. ResultsWe demonstrate that short-range sequence context-as short as a single "maximal" match- distinguishes primary orthologs from other homologs across whole genomes. On mammalian whole genomes not preprocessed by repeat-masker, potential orthologs are extracted by genome intersection as "non-nested maximal matches:" maximal matches that are not nested into other maximal matches. It emerges that on both nucleotide and gene scales, non-nested maximal matches recapitulate primary or positional orthologs with high precision and high recall, while the corresponding computation consumes less than one thirtieth of the computation time required by commonly applied whole-genome alignment methods. In regions of genomes that would be masked by repeat-masker, non-nested maximal matches recover orthologs that are inaccessible to Lastz net alignment, for which repeat-masking is a prerequisite. mmRBHs, reciprocal best hits of genes containing non-nested maximal matches, yield novel putative orthologs, e.g. around 1000 pairs of genes for human-chimpanzee. ConclusionsWe describe an intersection-based method that requires neither repeat-masking nor alignment to infer evolutionary history of sequences based on short-range genomic sequence context. Ortholog identification based on non-nested maximal matches is parameter-free, and less computationally intensive than many alignment-based methods. It is especially suitable for genome-wide identification of orthologs, and may be applicable to unassembled genomes. We are agnostic as to the reasons for its effectiveness, which may reflect local variation of mean mutation rate

Ultrasound Strain Imaging to Assess the Biceps Brachii Muscle in Chronic Poststroke Spasticity

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/146591/1/jum14639_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146591/2/jum14639.pd

Phase sensitivity at the Heisenberg limit in an SU(1,1) interferometer via parity detection

We theoretically investigate the phase sensitivity with parity detection on an SU(1,1) interferometer with a coherent state combined with a squeezed vacuum state. This interferometer is formed with two parametric amplifiers for beam splitting and recombination instead of beam splitters. We show that the sensitivity of estimation phase approaches Heisenberg limit and give the corresponding optimal condition. Moreover, we derive the quantum Cram\'er-Rao bound of the SU(1,1) interferometer.Comment: 9 pages, 2 figures, 3 table

Regulation of vascular endothelial growth factor bioactivity in patients with acute lung injury

Background: Reduced bioactive vascular endothelial growth factor (VEGF) has been demonstrated in several inflammatory lung conditions including the acute respiratory distress syndrome (ARDS). sVEGFR-1, a soluble form of VEGF-1 receptor, is a potent natural inhibitor of VEGF. We hypothesised that sVEGFR-1 plays an important role in the regulation of the bioactivity of VEGF within the lung in patients with ARDS. Methods: Forty one patients with ARDS, 12 at risk of developing ARDS, and 16 normal controls were studied. Bioactive VEGF, total VEGF, and sVEGFR-1 were measured by ELISA in plasma and bronchoalveolar lavage (BAL) fluid. Reverse transcriptase polymerase chain reaction for sVEGFR-1 was performed on BAL cells. Results: sVEGFR-1 was detectable in the BAL fluid of 48% (20/41) of patients with early ARDS (1.4– 54.8 ng/ml epithelial lining fluid (ELF)) compared with 8% (1/12) at risk patients (p = 0.017) and none of the normal controls (p = 0.002). By day 4 sVEGFR-1 was detectable in only 2/18 ARDS patients (p = 0.008). Patients with detectable sVEGFR-1 had lower ELF median (IQR) levels of bioactive VEGF than those without detectable sVEGFR-1 (1415.2 (474.9–3192) pg/ml v 4761 (1349–7596.6) pg/ml, median difference 3346 pg/ml (95% CI 305.1 to 14711.9), p = 0.016), but there was no difference in total VEGF levels. BAL cells expressed mRNA for sVEGFR-1 and produced sVEGFR-1 protein which increased following incubation with tumour necrosis factor a. Conclusion: This study shows for the first time the presence of sVEGFR-1 in the BAL fluid of patients with ARDS. This may explain the presence of reduced bioactive VEGF in patients early in the course of ARDS